The present invention relates to methods for the treatment and/or prophylaxis of diseases caused by tissue-adhering pilus-forming bacteria by interaction with the binding between pilus subunits and periplasmic chaperones. The invention further relates to methods for identifying/designing substances capable of interacting with periplasmic chaperones and methods for identifying binding sites in periplasmic chaperones. Finally, the invention relates to novel substances capable of interacting with periplasmic chaperones as well as pharmaceutical preparations comprising substances capable of interacting with periplasmic chaperones.
Pathogenic Gram-negative bacteria cause a number of pathological conditions such as bacteraemia, bacteria-related diarrhoea, meningitis and (very commonly) urinary tract infections, i.a. pyelonephritis, cystitis, urethritis etc.
Urinary tract infections are one of the major causes of morbidity in females. Despite the overall importance of urinary tract infections in women, there have been few efforts to apply novel strategies in order to treat and/or prevent these diseases. Commonly, conventional antibiotics are used to treat these infections, such as treatment with penicillins, cephalosporins, aminoglycosides, sulfonamides and tetracyclines; in the special case of urinary tract infections, urinary antiseptics such as nitrofurantoin and nalidixic acid are employed, too. However, emerging antibiotic resistance will in the future hamper the ability to successfully treat urinary tract infections. Multiple antibiotic resistance among these uropathogens is increasing. It has been estimated that the annual cost for evaluation and treatment of women with urinary tract infections exceeds one billion dollars. In addition, approximately one-fourth of the yearly 4 billion dollar cost attributed to nosocomial infections is a consequence of urinary tract infections. Among the causative agents of urinary tract infections, Escherichia coli clearly predominates among Gram-negative bacteria.
Pathogenic gram negative bacterial notably Escherichia coli, Haemophilus influenzae, Salmonella enteriditis, Salmonella typhimurium, Bordetella pertussis, Yersinia pestis, Yersinia enterocolitica, Helicobacter pylori, and Klebsiella pneumoniae owe part of their infectability to their ability to adhere to various epithelial tissues. Thus, e.g. E. coli adhere to the epithelial cells in the upper urinary tract in spite of the flushing effect of unidirectional flow of urine from the kidneys.
As indicated above, the above mentioned bacteria are involved in a variety of diseases: Urinary tract infections (E. coli), acute diarrhoea (E. coli, Y. enterocolitica and Salmonella spp), meningitis (E. coli and H. influenzae), whooping cough (B. pertussis), plague (Y. pestis), pneumonia and other respiratory tract infections (K. pneumoniae, H. influenzae) and peptic ulcer (H. pylori).
The initiation and persistence of many bacterial infections such as those described above is thought to require the presentation of adhesins on the surface of the microbe in accessible configurations which promote binding events that dictate whether extracellular colonization, internalization or other cellular responses will occur. Adhesins are often components of the long, thin, filamentous, heteropolymeric protein appendages known as pili, fimbriae, or fibrillae (these three terms will be used interchangeably herein) The bacterial attachment event is often the result of a stereo-chemical fit between an adhesin frequently located at the pilus tip and specific receptor architectures on host cells, often comprising carbohydrate structures in membrane associated glycoconjugates.
Uropathogenic strains of E. coli express P and type 1 pili that bind to receptors present in uroepithelial cells. The adhesin present at the tip of the P pilus, PapG (pilus associated polypeptide G), binds to the Galxcex1(1-4)Gal moiety present in the globoseries of glycolipids, while the type 1 adhesin, FimH, binds D-mannose present in glycolipids and glycoproteins. Adhesive P pili are virulence determinants associated with pyelonephritic strains of E. coli whereas type 1 pili appear to be more common in E. coli causing cystitis. At least eleven genes are involved in the biosynthesis and expression of functional P pili; the DNA sequence of the entire pap gene cluster has been determined. P pili are composite heteropolymeric fibers consisting of flexible adhesive fibrillae joined end to end to pilus rods. The pilus rod is composed of repeating PapA protein subunits arranged in a right handed helical cylinder. Tip fibrillae which extend from the distal ends of each pilus rod were found to be composed mostly of repeating subunits of PapE arranged in an open helical conformation. The PapG adhesin was localized to the distal ends of the tip fibrillae, a location which is assumed to maximize its ability to recognize glycolipid receptors on eukaryotic cells. Two minor pilus components, PapF and PapK, are specialized adaptor proteins found in the tip fibrillum. PapF links the adhesin moiety to the fibrillum while PapK joins the fibrillum to the pilus rod. The composite architecture of the P pilus fibre reveals the strategy used by uropathogenic E. coli to present the PapG adhesin to eukaryotic receptors. The rigid PapA rod extends the adhesin away from interference caused by LPS and other components at the bacterial cell surface while the flexible fibrillum allows PapG steric freedom to recognize and bind to the digalactoside moiety on the uroepithelium. With a few exceptions, the structural organization of type 1 pili is very similar to that described for P pili. In type 1 pili, the mannose binding fibrillar tip adhesin is known as FimH.
The assembly of virulence-associated pili in Gram-negative pathogens requires the function of periplasmic chaperones. Molecular chaperones are vital components of all living cells, prokaryotic and eukaryotic. Chaperones serve a variety of cellular functions including folding, import and export of proteins in various cellular compartments (Gething and Sambrook, 1992). Thus, a periplasmic chaperone is a molecular chaperone which exerts its action in the periplasmic space in bacteria.
PapD and FimC are the periplasmic chaperones that mediate the assembly of P and type 1 pili, respectively. Detailed structural analyses have revealed that PapD is the prototype member of a conserved family of periplasmic chaperones in Gram-negative bacteria. These chaperones have a function which is part of a general strategy used by bacteria to cap and partition interactive subunits imported into the periplasmic space into assembly competent complexes, making non-productive interactions unfavourable. Determination of the three-dimensional structure of PapD revealed that it consists of two immunoglobulin-like domains oriented in a boomerang shape such that a cleft is formed. PapD binds to each of the pilus subunit types as they emerge from the cytoplasmic membrane and escorts them in assembly-competent, native-like conformations from the cytoplasmic membrane to outer membrane assembly sites comprised of PapC. PapC has been termed a molecular usher since it receives chaperone-subunit complexes and incorporates, or ushers, the subunits from the chaperone complex into the growing pilus in a defined order.
With the exception of the type IV class of pili, all other genetically well characterized pilus systems in Gram-negative prokaryotes contain a gene analogous to PapD (Normark et al., 1986; Hultgren et al. 1991); cf. also table A. FanE, faeE, sfaE, ClpE and f17-D have been sequenced (Lintermans, 1990; Schmoll et al., 1990; Bertin Y et al., 1993; Bakker et al., 1991) and encode pilus chaperones required for the assembly of K99, K88, S and F17 pili, respectively, in E. coli. The assembly of Klebsiella pneumoniae type 3 pili and Haemophilus influenzae type b pili requires the mrkb and hifB gene products, respectively (Gerlach et al., 1989,; Allen et al., 1991). The structure-function relationships of all of these chaperones have been analyzed using their amino acid sequences and information from the crystal structure of PapD (Anders Holmgren et al., 1992). The results have provided insight into the molecular intricacies that have been evolutionarily conserved in this class of proteins and suggested significant structural similarities to immunoglobulins.
PapD is thus the prototype member of a family of periplasmic chaperone proteins which are necessary for the correct supramolocular assembly of bacterial pili. Chaperones such as PapD in E. coli are required to bind the above-mentioned pilus proteins imported into the periplasmic space, partition them into assembly competent complexes and prevent non-productive aggregation of the subunits in the periplasm (Dodson et al. 1993).
In the absence of an interaction with the chaperone, pilus subunits aggregate and are proteolytically degraded (Kuehn, Normark, and Hultgren, 1991). It has recently been discovered (Strauch, Johnson and Beckwith, 1989) that the DegP protease is greatly responsible for the degradation of pilin subunits in the absence of the chaperone. This discovery has allowed the elucidation of the fate of pilus subunits expressed in the presence or absence of the chaperone using monospecific antisera in western blots of cytoplasmic membrane, outer membrane and periplasmic proteins prepared according to standard procedures. Expression of papG or papA in the degP41 strain (a DegPxe2x88x92 E. coli strain) in the absence of a chaperone was toxic to the bacteria due to the accumulation of these proteins in the cytoplasmic membrane suggesting that the chaperone was required for subunit import into the periplasmic space. The severity of the growth defect was related to the level of expression of the pilin subunit, and was generally more dramatic with PapG than PapA. Co-expression of PapD under the control of the inducible arabinose promoter rescued the growth defect associated with subunit expression in the degP41 strain and allowed PapG to be imported into the periplasm.
Up to this time, little has been elucidated about the molecular recognition motifs of chaperones. Cytoplasmic chaperones such as SecB, GroEL and DNaK bind to a diverse group of unfolded target proteins in a sequence independent manner (Gething and Sambrook, 1992). Recently, it has been suggested that DNaK binds mainly via the target""s peptide backbone (Landry et al., 1992) and that GroEL may rely more on side-chain hydrophobicity and the ability of the target sequence to form an amphipathic xcex1-helix (Landry and Gierasch, 1991). PapD differs, however, in that it seems to bind its target proteins in folded conformations (Kuehn et al., 1991).
The three-dimensional structure of PapD has previously been solved (Holmgren and Brxc3xa4nden, 1989). This has shown PapD to consist of two globular domains positioned such that the overall shape of the molecule resembles a boomerang with a cleft between the two domains. Each domain is a xcex2-barrel structure formed by two antiparallel xcex2-pleated sheets, packed tightly together to form a hydrophobic core, with a topology similar to that of an immunoglobulin fold. The N-terminal domain of PapD most resembles an Ig variable domain whilst the C-terminal domain of PapD resembles CD4 (Wang et al., 1990, Ryu et al., 1990) and the human growth hormone receptor (de Vos et al., 1992).
A structural alignment between PapD and several periplasmic chaperones predicted to have a similar immunoglobulin-like structure has identified invariant, highly conserved and variable residues within this protein family (Holmgren et al., 1992). Most conserved residues seem to participate in maintaining the overall structure and orientation of the domains towards one another. However, two conserved residues, Arg-8 and Lys-112 are surface exposed and oriented towards the cleft between the domains. Site-directed mutagenesis of the Arg-8 amino acid has shown that it form at least part of the pilus subunit binding pocket (Holmgren et al., 1992; Kuehn et al., 1993).
From a sequence analysis of a number of the above-mentioned pilus subunit proteins, it has been observed that they possess a number of common features including homologies at the C termini (see also example 2). It is thought that these similarities in sequence may be responsible for some function common to all the pilus proteins, such as binding to their periplasmic chaperone. Indeed, the C-terminal region of the P-pili adhesin PapG has already been shown to be important in the in vivo binding to PapD (Hultgren et al., 1989). Table A lists 16 periplasmic proteins, all involved in assembly of cell surface structures in pathogenic bacteria and all with significant homology with PapD.
In summary, the three-dimensional structure of PapD as well as the function of PapD and other periplasmic chaperones are known, whereas the exact motif of binding between PapD and the pilus subunits has been unknown until now.
According to the present invention, it has been realized that the above-mentioned characteristics of PapD and other related chaperones make them interesting targets for drugs designed primarily to reduce the pathogenicity of bacteria which adhere by means of pili; for example, a drug which blocks the binding between a chaperone and the pilus-subunits (thereby interfering with the assembly of the intact pilus) will interfere with the formation of intact pili, thereby reducing bacterial capacity to adhere to host epithelium.
In order to design such a drug it is of great value that the motif of binding between the chaperone and the pilus protein(s) is known in detail, in order to develop the method to effectively identify compounds capable of blocking this binding.
An aspect of the current invention relates to a method for the treatment and/or prophylaxis of diseases caused by tissue-adhering pilus-forming bacteria, comprising preventing, inhibiting or enhancing binding between at least one type of pilus subunit and at least one type of molecular chaperone in the pilus-forming bacteria, which molecular chaperone binds pilus subunits during transport of these pilus subunits through the periplasmic space and/or during the process of assembly of the intact pilus.
As used herein, the term xe2x80x9cpilusxe2x80x9d, xe2x80x9cfimbriaxe2x80x9d, or xe2x80x9cfibrillaxe2x80x9d, relates to fibrillar heteropolymeric structures embedded in the outer membrane of many tissue-adhering pathogenic bacteria, notably the pathogenic gram negative bacteria. In the present specification the terms pilus, fibrillum and fimbria will be used interchangeably. A pilus is, as explained above, composed of a number of xe2x80x9cpilus subunitsxe2x80x9d, which constitute distinct functional parts of the intact pilus. A very important pilus subunit is the xe2x80x9cadhesinxe2x80x9d, the pilus subunit which is responsible for the tissue-binding capacity of the bacterium.
By the term xe2x80x9cmolecular chaperonexe2x80x9d is meant a molecule which in living cells has the responsibility of binding to peptides in order to mature the peptides in a number of ways. Many molecular chaperones are involved in the process of folding of peptides into their native conformation whereas other molecular chaperones are involved in the process of export out of or import into the cell of peptides. Specialized molecular chaperones are xe2x80x9cperiplasmic chaperonesxe2x80x9d, which are bacterial molecular chaperones exerting their main actions in the xe2x80x9cperiplasmic spacexe2x80x9d (the space between the inner and outer bacterial membrane). Periplasmic chaperones are involved in the process of correct assembly of intact pili. When used herein, the simple term xe2x80x9cchaperonexe2x80x9d designates a molecular, periplasmic chaperone if nothing else is indicated.
When using the phrase xe2x80x9cone type ofxe2x80x9d is meant that the pilus subunit or the chaperone in question is of one distinct species. However, especially the fact that there is extensive homology between different species of periplasmic molecular chaperones renders it likely that the interference with one type of chaperone using e.g. a compound will make it possible to also use the compound in interference with other chaperones.
The phrase xe2x80x9cpreventing, inhibiting or enhancing binding between pilus subunits and at least one molecular chaperone in the pilus-forming bacteriaxe2x80x9d indicates that the normal interaction between a chaperone and its natural ligand, i.e. the pilus subunit, is being affected either by being completely or substantially completely prevented, or by being inhibited, or expressed in another manner, reduced to a such an extent that the binding of pilus subunits to the chaperone is measurably lower than is the case when the chaperone is interacting with the pilus subunit at conditions which are substantially identical (with regard to pH, concentration of ions and other molecules) to the native conditions in the periplasmic space. Similarly, the enhancement of binding between the chaperone and the pilus subunit should be such that the binding of pilus subunits to the chaperone is measurably higher than is the case when the chaperone is interacting with the pilus subunit at conditions which are substantially identical (with regard to pH, concentration of ions and other molecules) to the native conditions in the peri-plasmic space. Measurement of the degree of binding can be determined in vitro by methods known to the person skilled in the art (microcalormetry, radioimmunoassays, enzyme based immuno assays, etc).
It should, on the basis of the above, be clear that prevention or inhibition of the normal interaction between a pilus subunit and a chaperone should have a substantially limiting effect on pilus assembly. However, an enhancement of the binding between pilus subunits and chaperones may also prove to be devastating to a bacterium. As will appear from example 2, different pilus subunits bind to PapD with different affinities and affecting this narrowly balanced system may also cause a limitation on the rate and efficiency of pilus assembly.
It is believed that even modest changes in the binding between pilus subunits and chaperones can have dramatic impact on the efficiency of pilus assembly, and thus on the ability of the bacteria to adhere. For example, if the change in the binding between a chaperone and one pilus subunit is such that the normal order of affinities between the chaperones and the pilus subunits which normally bind thereto is altered, then the normal assembly of the pilus should be disturbed, since the order of assembly of the pilus may be dependent i.a. on the affinities between the pilus subunits and the chaperone: The pilus subunits with the highest affinities to the chaperone may be incorporated before other pilus subunits with lesser affinities.
Thus, prevention, inhibition or enhancement of binding between pilus subunits and a periplasmic molecular chaperone have the effect of impairing pilus assembly, whereby the infectivity of the microorganism normally expressing the pili is reduced.
Prevention, inhibition or enhancement of the binding between pilus subunits can be accomplished in a number of ways. A preferred method according to the invention of treatment and/or prophylaxis of diseases caused by tissue-adhering pilus-forming bacteria is to administer an effective amount of a substance to a subject in need thereof, the substance being capable of interacting with at least one type of molecular chaperone which binds pilus subunits during transport of these pilus subunits through the periplasmic space and/or during the process of assembly of the intact pilus, in such a manner that binding of pilus subunits to the molecular chaperone is prevented, inhibited or enhanced.
The substance can be any compound which has one of the above mentioned effects on the interaction between chaperones and pilus subunits and thereby on the assembly of the pilus. Especially interesting substances are those which are likely to interact with the pilus subunit binding part of the chaperone, but interaction with other sites in the chaperones may also cause prevention, inhibition or enhancement of the binding between pilus subunits and the chaperone. This can be an effect of direct steric blocking of the normal binding between the subunit and the chaperone, but it may also be an effect of a conformational change in the chaperone. A method of identifying substances to be used in the method of the invention is disclosed below.
The interaction between the substance and the chaperone may be a covalent as well as a non-covalent binding to the chaperone by the substance.
By the term xe2x80x9csubject in need thereofxe2x80x9d is in the present context meant a subject, which can be any animal, including a human being, who is infected with, or is likely to be infected with, tissue-adhering pilus-forming bacteria which are believed to be pathogenic.
By the term xe2x80x9can effective amountxe2x80x9d is meant an amount of the substance in question which will in a majority of patients have either the effect that the disease caused by the pathogenic bacteria is cured or, if the substance has been given prophylactically, the effect that the disease is prevented from manifesting itself. The term xe2x80x9can effective amountxe2x80x9d also implies that the substance is given in an amount which only causes mild or no adverse effects in the subject to whom it has been administered, or that the adverse effects may be tolerated from a medical and pharmaceutical point of view in the light of the severity of the disease for which the substance has been given.
The route of administration of the substance could be any conventional route of administration, i.e. oral, intraveneous, intramuscular, intradermal, subcutaneous etc. The oral route is preferred.
The dosage of such a substance is expected to be the dosage which is normally employed when administering antibacterial drugs to patients or animals, i.e. 1 xcexcg-1000 xcexcg per kilogram of body weight per day. The dosage will depend partly on the route of administration of the substance. If the oral route is employed, the absorption of the substance will be an important factor. A low absorption will have the effect that in the gastro-intestinal tract higher concentrations, and thus higher dosages, will be necessary. Also, the dosage of such a substance when treating infections of the central nervous system (CNS) will be dependent on the permeability of the blood-brain barrier for the substance. As is well-known in the treatment of bacterial meningitis with penicillin, very high dosages are necessary in order to obtain effective concentrations in the CNS.
It will be understood that the appropriate dosage of the substance should suitably be assessed by performing animal model tests, wherein the effective dose level (e.g. ED50) and the toxic dose level (e.g. TD50) as well as the lethal dose level (e.g. LD50 or LD10) are established in suitable and acceptable animal models. Further, if a substance has proven efficient in such animal tests, controlled clinical trials should be performed. Needless to state that such clinical trials should be performed according to the standards of Good Clinical Practice.
Although the preferred way of preventing, inhibiting or enhancing the binding between pilus subunits and chaperones is to administer a substance with the above mentioned effects on the chaperone, other ways are possible. For instance, substances interacting with one type of pilus subunit could also have the effects described above, and for the same reasons. However, as the interaction with the chaperone is likely to exert effects on the assembly into the pilus of most, if not all, pilus subunits constituting the intact pilus, it is expected that the interaction with the chaperone will be the most efficient in terms of hampering bacterial infectivity.
As will appear from the examples below, most of the data on binding between chaperones and pilus subunits have been obtained by studying the interaction between the PapD chaperone from E. coli. However, since many tissue adhering bacteria have been found to express pili which share substantial homologies in their C-terminal part, and since substantial homologies have been demonstrated between the various periplasmic chaperones which until now have been isolated (see table A), it is justified to assume that some substances and classes of substances will be capable of interacting with the majority of existing periplasmic chaperones and thus be useful in the treatment and/or prophylaxis of diseases caused by the bacteria harbouring these chaperones when the substance is administered to patients infected with the bacteria.
Thus, the method of the invention for the treatment and/or prophylaxis is especially intended to be used in patients which are infected by bacteria selected from the group consisting of Haemophilus spp, Helicobacter spp, Pseudomonas aeruginosa, Mycoplasma spp, and all members of the Enterobacteriacieae family, including Escherichia spp, Salmonella spp, Bordetella spp, Yersinia spp, Proteus spp and Klebsiella spp. In this connection, especially the bacteria selected from the group consisting of E. coli, Y. pestis, Y. enterocolitica, B. pertussis, K. pneumoniae, S. typhimurium, S. typhi, S. paratyphii, Helicobacter pylori, Proteus mirabilis and Haemophilus influenzae are regarded as infectants which cause infections which can be treated and/prevented by the use of the method according to the invention.
Accordingly, in important aspects of the invention, the binding of a pilus subunit to a chaperone selected from the group consisting of PapD, FimC, SfaE, FaeE, FanE, Cs3-1, F17D, ClpE, EcpD, Mrkb, FimB, SefB, HifB, MyfB, PsaB, PefD, YehC, MrpD, CssC, NfaE, AggD, and Caf1M is prevented, inhibited or enhanced. It is especially preferred that the binding of PapD to at least one pilus subunit is affected.
As stated above, in a preferred embodiment of the invention, the prevention, inhibition or enhancement of the binding is accomplished by interacting with, in the molecular chaperone, a binding site which is normally involved in binding to pilus subunits during transport of these pilus subunits through the periplasmic space and/or during the process of pilus assembly.
As mentioned, in connection with the present invention, the binding motif between PapD and a peptide which constitute the 19 amino acids of the C-terminal of PapG (G1xe2x80x2-19xe2x80x2), a pilus subunit, has been determined. As is described in detail herein, other chaperones share substantial homologies with PapD in this binding site. Thus, such a binding site is of great interest as a target for drugs which are intended to interact with periplasmic chaperones. Therefore, in a preferred embodiment of the above described methods of the invention, the binding site which is affected is one which binds G1xe2x80x2-19xe2x80x2.
Thus, an important aspect of the invention is a method as described above, wherein the binding site is a binding site to which the carboxyl terminal part of a pilus subunit is capable of binding, and which comprises site points substantially identical to the invariant residues Arg-8 and Lys-112 in PapD, and a polypeptide fragment which is capable of interacting with a xcex2-strand of the carboxyl terminal part of the pilus subunit thereby stabilizing the binding of said subunit at the Arg-8 and Lys-112 site points of the binding site. An especially preferred aspect of the invention is a method as described above, where the binding side is the G-protein binding site of PapD as described herein.
The term xe2x80x9csite-pointxe2x80x9d refers to a chemical group with well defined physical/chemical characteristics such as size, charge, hydrophobicity/hydrophilicity, polarity, direction of hydrogen bonds as well as a 3-dimensional position (distance and angle) relative to other such chemical groups. Thus site-points which are xe2x80x9csubstantially identicalxe2x80x9d to Arg-8 and Lys-112, are chemical groups which substantially share the same well-defined physical/chemical characteristics as these two amino acids.
The term xe2x80x9cinvariant residuesxe2x80x9d refer to amino acid residues which can be found in a number of proteins without there being any variation with regard to the precise type of the amino acid and without there being any substantial variation in their function in the proteins. The presence of invariant residues in a large number of related proteins normally is an indication of the biological importance of such residues, since mutations lacking these residues apparently lacks the function of the intact protein, too. As described herein, it has been found that all periplasmic molecular chaperones share the amino acid residues which are equivalent to Arg-8 and Lys-112. It is believed that these two residues therefore are of considerable importance to pilus-forming bacteria.
xe2x80x9cA polypeptide fragment capable of interacting with a xcex2-strand of the carboxyl terminal part of a pilus subunitxe2x80x9d indicates that part of the chaperone (which is also a part of the binding site) is capable of interacting with a xcex2-strand of the pilus subunit. This interaction serves as a stabilizing factor in the binding between the pilus subunit and the chaperone and is considered a very important part of the total motif of binding between the chaperone and the pilus subunit. Further, it has recently been rendered probable by the inventors that the xcex2-strand serves as a template for the correct folding of the pilus subunit (cf. example 10).
As explained herein, the C-terminal part of many, if not all, known pilus subunits, share substantial homologies, which is another indication of the importance of the 3-dimensional structure of the pilus subunit as well as of the chaperone in order for the binding to take place and be stable.
As appears from the examples, another binding site residing in domain 2 of PapD has been identified. This binding site interacts with fusion protein MBP-G1xe2x80x2-140xe2x80x2 as well as with a short peptide constituted of the C-terminal amino acid residues 125xe2x80x2to 140xe2x80x2 of PapG. Thus, also this binding site is of great interest as a target for drugs which are intended to interact with periplasmic chaperones. Therefore, a preferred embodiment of the above described methods of the invention is a method wherein the binding site which is affected is one which binds either of the two above-described peptides.
It will be understood that the above-described methods comprising administration of substances in treating and/or preventing diseases are dependent on the identification or de novo design of substances which are capable of exerting effects which will lead to prevention, inhibition or enhancement of the interaction between pilus subunits and periplasmic molecular chaperones. It is further important that these substances will have a high chance of being therapeutically active.
Thus, an aspect of the invention relates to a method for identifying a potentially therapeutically useful substance capable of interacting with a periplasmic molecular chaperone, thereby preventing, inhibiting or enhancing the interaction between a periplasmic molecular chaperone and a pilus subunit, the method comprising at least one of the following steps:
1) testing a candidate substance in an assay in which the possible prevention, inhibition or enhancement by the substance of the interaction between the periplasmic molecular chaperone and the pilus subunit is determined by
a) adding the substance to a system comprising the periplasmic molecular chaperone or an analogue thereof in an immobilized form and the pilus subunit or an equivalent thereof in a solubilized form and determining the change in binding between the pilus subunit or equivalent thereof and the periplasmic molecular chaperone or analogue thereof caused by the addition of the substance, or
b) adding the substance to a system comprising the pilus subunit or an equivalent thereof in an immobilized form and the periplasmic molecular chaperone or an analogue thereof in a solubilized form and determining the change in binding between the pilus subunit or equivalent thereof and the periplasmic molecular chaperone or analogue thereof caused by the addition of the substance, or
c) adding the substance to a system comprising the pilus subunit or an equivalent thereof as well as the periplasmic molecular chaperone or an analogue thereof in solubilized form and determining the change in binding between the pilus subunit or equivalent thereof and the periplasmic molecular chaperone or analogue thereof caused by the addition of the substance, or
d) adding the substance to a system comprising the pilus subunit or an equivalent thereof as well as the periplasmic molecular chaperone or an analogue thereof in solubilized form and measuring the change in binding energy caused by the addition of the substance, and identifying the substance as potentially therapeutically useful if a significant change in the binding energy between the pilus subunit or equivalent thereof and the periplasmic molecular chaperone or analogue thereof is observed,
and identifying the substance as potentially therapeutically useful if a significant change in the binding or binding energy between the pilus subunit or equivalent thereof and the periplasmic molecular chaperone or analogue thereof is observed;
2) testing a candidate substance in an assay in which the possible prevention, inhibition or enhancement of the interaction between the periplasmic molecular chaperone and the pilus subunit is determined by
adding the substance to a system comprising living tissue-adhering pilus-forming bacteria followed by determination of the growth rate of the bacteria; a reduction in growth rate compared to a corresponding system wherein the substance has not been added being indicative of prevention, inhibition or enhancement of the binding between the periplasmic molecular chaperone and the pilus subunit, or
adding the substance to a system comprising living tissue-adhering pilus-forming bacteria followed by a determination of the tissue adhesion of the bacteria, a reduction in tissue adhesion compared to a corresponding system wherein the substance has not been added being indicative of prevention, inhibition or enhancement of the binding between the periplasmic molecular chaperone and the pilus subunit,
and identifying the substance as potentially therapeutically useful if a reduction in growth rate or tissue adhesion is observed after the addition of the substance; and
3) administering, to an experimental animal, a substance which has been established in vitro to prevent, inhibit or enhance the interaction between a periplasmic molecular chaperone and a pilus subunit, the experimental animal being inoculated with tissue-adhering pilus-forming bacteria before, simultaneously with or after the administration of the substance, and electing as a substance suitably capable of interacting with a periplasmic molecular chaperone, a substance preventing and/or curing and/or alleviate disease caused by the bacteria.
By the term xe2x80x9can equivalent of a pilus subunitxe2x80x9d is meant a compound which has been established to bind to the chaperone in a manner which is comparable to the way the pilus subunit binds to the chaperone, e.g. by the demonstration of the pilus subunit and the equivalent competing for the binding to the chaperone. Preferred equivalents of pilus subunits are G1xe2x80x2-19xe2x80x2WT, MBP-G1xe2x80x2-140xe2x80x2 and G125xe2x80x2-140xe2x80x2, which are all described in detail herein.
The term xe2x80x9can analogue of a chaperonexe2x80x9d denotes any substance which have the ability of binding at least one pilus subunit in a manner which corresponds to the binding of said chaperone to a pilus subunit. Such an analogue of the chaperone can be a truncated form of the intact chaperone (e.g. one of the two domains of PapD) or it can be a modified form of the chaperone which may e.g. be coupled to a probe, marker or another moiety. Finally, the analogue of the chaperone can be an isolated, but partially or fully functional, binding site of the chaperone or a synthetic substance which mimics such a binding site.
The immobilization mentioned above may be simple non-covalent binding to an adhering surface or a host or receptor molecule such as an antibody, or covalent binding to a spacer molecule such as a polymer or a peptide.
In the above mentioned step 1a), the pilus subunit or the equivalent thereof being bound to the periplasmic molecular chaperone or an analogue thereof can be detected in a number of ways, e.g. by the pilus subunit or the equivalent thereof being labelled, or by means of a labelled ligand (such as an antibody) capable of reacting with the pilus subunit or the equivalent thereof, or by means of a refractive index based determination of the extend of binding, such as the Pharmacia BiaCore(copyright) assay.
Accordingly, in step 1b) the periplasmic molecular chaperone or the analogue thereof being bound to the pilus subunit or the equivalent thereof may be detected by the periplasmic molecular chaperone or the analogue thereof being labelled, by means of a labelled ligand (e.g. antibody) capable of reacting with the periplasmic molecular chaperone or the analogue thereof, or by means of a refractive index based determination of the extend of binding, such as the Pharmacia BiaCore(copyright) assay.
In step 1c) the periplasmic molecular chaperone or the analogue thereof being bound to the pilus subunit or the equivalent thereof may be detected by separation of pilus subunit/chaperon complexes (e.g. by ultracentrifugation, ultrafiltration, liquid chromatography, such as size exclusion chromatography, or electrophoresis). Described below is a method relying on the changes in fluorescence of a short PapG fragment when this fragment is bound to PapD. This method is a preferred assay in the method of the invention.
The determination of binding energy in step 1c) is preferably performed in a microcalorimetric system using the well-known technique of microcalorimetry.
The above-indicated steps serve 3 purposes. The types of assays in step 1) are intended to shed light over the ability of the candidate substance of interacting with the chaperone. In the instances wherein labelled substances, chaperones or antibodies are used, the label could be a radioactive label, a fluorescent or light absorbing label, an enzyme such as horse-radish peroxidase, a ligand such as biotin, or any other conventional labelling system known to the person skilled in the art. The detection of the labelled compound is then dependent on the choice of label: radioactivity may be measured in a liquid-scintillation counter, a gamma counter, or any other convenient detection system for radioactivity, enzyme-labels are detected by the presence or absence of a specific substrate for the enzyme (optical density assessment, chemical reactivity of the remaining substrate or of the product etc.), fluorescent labels may be detected by fluorescence microscopy or simple measurement of the fluorescent emission, light-absorbing labels may be detected by measurement of absorbtion of light of a characteristic wavelength, and biotin may be detected by its binding to streptavidin.
The separation of high molecular complexes by ultracentrifugation or ultrafiltration in 1) may be detected by one of the components of the complex being labelled as described above; it is thus possible to detect the ratio between bound and unbound pilus subunit/equivalent, but the detection step may also rely on the binding of antibodies to one of the components of the complex, and the subsequent detection of this antibody. Any conventional chromatographic technique may be employed (HPLC, FPLC, size exclusion, etc) The separation by electrophoresis may e.g. be performed by capillary electrophoresis.
The assays in step 2) all relate to the effects of the candidate substance on bacterial activity in vitro. The demonstration of a reduction in growth rate of the bacteria or a demonstration of reduced adherence to cells or synthetic surfaces in an assay of course cannot be contributed to the effect of interaction with chaperones only, but a demonstration of this kind should provide a good estimate of the potential therapeutical usefulness of such a substance.
The determination of growth rate may be performed by counting of colonies on solid agar plates striped with the bacteria, by counting bacterial density in liquid growth media (OD600 determination), by measuring fluorescence of substances such as NAD(P)H, ATP, or amino acids, which are contained in the bacterial cells only, or by any other convenient detection system known to the person skilled in the art. The determination of adherence of the bacteria may be performed in a similar manner after the adhering bacteria have been isolated. A determination of adherence is preferably performed by measuring the ability of the bacteria to agglutinate red blood cells or receptor-coated latex beads, by measuring the bacterial adhesion to receptor-coated microtiter plates, or by measuring the bacterial adhesion to other synthetic surfaces.
In a preferred embodiment of the method described above, the living, tissue adhering pilus-forming bacteria are of a protease deficient strain, the protease being one which is at least partially responsible for the degradation of pilus subunits. One especially preferred type of strain is the degP41 strain of E. coli. As described herein, the degP41 strain lacks activity of the DegP protease which is responsible for degradation of pilus subunits in the E. coli when these are not rescued into periplasmic space by PapD, and degP41 strains are thus especially sensitive to changes in the efficiency of PapD, as the accumulation of pilus subunits is toxic to the cell. It is believed that equivalent proteases exist in other pilus expressing bacteria.
The animal study in step 3) is performed in order to demonstrate the potential therapeutic usefulness of the candidate substance in vivo. Further, as already mentioned above, such animal studies should also establish the a priori values regarding effective dosage and toxicity before the candidate substance finally is tested in human beings in controlled clinical trials. The animal studies should also provide information regarding the convenient formulation of the substance in a pharmaceutical preparation as well as the preferred route of administration, as it is possible to obtain, from the animal model, data for absorbtion of the substance as well as data for the metabolism and excretion of the substance. The experimental animal is preferably a mouse, a rat, a cat, a dog, a monkey, a horse, a cow, a pig, or a chicken.
The term xe2x80x9csuitably capable of interacting with a molecular chaperonexe2x80x9d is intended to indicate that a substance, apart from being capable of interacting with a molecular chaperone, also is capable of exerting effects in an in vivo system, i.e. that the substance in addition to its binding capability also exhibits compatibility with a biological system, i.a. a patient.
Although the above-indicated in vivo studies, especially the experiments in animal models, are the best indicators of the potential therapeutical usefulness of a substance in the prevention, inhibition, or enhancement of the binding between a chaperone and a pilus subunit, it should not be forgotten that the in vitro assays outlined above serve as important leads when developing compounds with a therapeutical potential. If one relied only on in vivo assays, it is very likely that compounds which in fact exhibit the desired effect on the chaperone/pilus subunit interaction would be screened out by the in vivo assays, because these compounds could lack e.g. the ability to penetrate biological membranes. When using the in vitro assays, a much greater chance of finding a lead compound is maintained.
The evaluation of the effect of a substance tested in the in vitro assays described herein (cf. in this connection especially the examples) depends on a number of factors. It will be understood by the skilled person that a small molecule could be added in rather high molar concentrations in order to exert an effect on the chaperone/pilus subunit interaction (and even then the small molecule may still be an interesting lead compound), whereas larger molecules may exert marked effects even in rather low molar concentrations. In general, when any in vitro assay described herein is regarded as having a positive result when testing a candidate substance (i.e. that the substance tested shows a xe2x80x9csignificantxe2x80x9d effect), the following condition should be fulfilled: The compound should exert a significant effect on pilus subunit/chaperone interaction (or on an interaction in an equivalent system which correlates well to pilus subunit/chaperone interaction), the significant effect being one which with no doubt can be attributed to the interaction between the substance and the chaperone and which is not an unspecific interaction between the chaperone and the substance (due to e.g. radical changes in the physical and chemical environment when the substance is added). One way of excluding unspecific interactions as the reason for the exerted effect is to use at least one control which is a chemically comparable substance (with respect to molecular mass, charge/polarity and gross 3-dimensional conformation (globular, fibrillar etc.). If the control does not result in substantially the same effect in the assay as the substance, it can be concluded that the substance must be regarded as an assay positive substance.
The assays described in the examples are all good examples of assay types, which could serve as the test system in the above-described method of the invention. However, it is preferred that the method described in example 10 employing a fluorescence labelled variant of a pilus subunit is used in step 1c). This assay may shortly be described a s follows:
adding the substance to a first system comprising the periplasmic molecular chaperone or an analogue thereof,
subsequently adding a pilus subunit or an equivalent thereof which has been labelled with an environmentally sensitive fluorescent probe,
determining the fluorescent emission at a particular wavelength which is indicative of the amount of binding between the periplasmic molecular chaperone or the analogue thereof and the pilus subunit or the equivalent thereof, and
comparing the determined fluorescent emission to fluorescent emission determined in a corresponding second system containing substantially the same concentrations of the molecular chaperone or the analogue thereof and the pilus subunit or the equivalent thereof but substantially no substance,
a significant difference in fluorescent emission between the first and second system being indicative of interaction between the periplasmic molecular chaperone or the analogue thereof and the substance.
The advantage of this assay is that it may be employed for quantitative determinations of the effect of the tested substance on the chaperone/pilus subunit system. By using this assay the inventors have e.g. determined the constant of binding between a PapG analogue and PapD. The quantitative determinations may be performed by performing the determination of fluorescent emission in the second system a plurality of times at varying molar ratios between the pilus subunit or the equivalent thereof and the periplasmic chaperone and the equivalent thereof, whereupon the constant of binding between the pilus subunit or equivalent thereof and the periplasmic molecular chaperone or analogue thereof is assessed from the determined fluorescent emission data. From the data obtained in this way it is also possible to determine the binding constant of the substance in a parallel manner, which will appear from claim 11.
It will be understood that the above-indicated method for identifying a potentially therapeutically useful substance is dependent on the actual presence of the substance. Normally, it is necessary to either purify or synthesize the candidate substance before it is subjected to the above-mentioned method. However, since many such candidate substances are likely to be tested before a substance which is suitably capable of interacting with a chaperone will be identified, it is of interest to identify such substances before they are subjected to the method above, thereby diminishing the resources spent on purification and/or synthesis steps.
Hence, the invention also relates to a method for identifying and/or designing a substance, X, capable of interacting with a chaperone, e.g. binding to the chaperone, with a predicted binding energy equal to or better than a predetermined threshold value, the method comprising
1) selecting a substance, A, which could potentially interact with a site in the chaperone, and providing a 3-dimensional structural representation thereof,
2) predicting the binding free energy between the substance A and the site in the chaperone,
3) if the predicted binding free energy between the substance A and the site in the chaperone is equal to or better than the predetermined threshold value, then identifying the substance A as the substance X,
4) if the predicted binding free energy between the substance A and the site in the chaperone is not equal to or better than a predetermined threshold value, then modifying the 3-dimensional structural representation and predicting the binding free energy between the thus modified substance, B, and the site in the chaperone, and
5) repeating step 4 until the predicted binding free energy determined between the resulting substance, X, and the site in the chaperone is equal to or better than the predetermined threshold value.
It is possible to expand the above-mentioned method with two further steps, wherein the actual binding free energy is determined, in order to establish that the experimental binding free energy also is better than the predetermined threshold value. By performing the following two steps
6) providing a sample of the chemical substance X and a sample of the chaperone and measuring the binding free energy between the chemical substance X and the chaperone (e.g. by microcalometry as mentioned above), and establishing that the measured binding free energy between the chemical substance X and the chaperone is equal to or better than the predetermined threshold value, and optionally
7) subjecting the substance X to the method mentioned above for identifying a substance suitably capable of interacting with a chaperone, in order to verify that the substance X is a potentially therapeutically useful substance capable of interacting with a chaperone, it is thus verified that the binding free energy between the candidate substance and the chaperone actually is better than the predetermined threshold value. Step 7) further establishes that the candidate substance stands good chances of being therapeutically useful.
The phrase xe2x80x9cpredicting the binding free energyxe2x80x9d is meant to imply that the binding free energy is determined by calculation rather than by performing experimental work determining the actual binding free energy. One (theoretical) way of predicting binding free energy is by performing free energy perturbation (FEP) calculations on the interacting substances, but because of the vast amount of calculations such an approach would have as a result it is preferred that the empirical approximative method described below is employed.
The term xe2x80x9cbetter thanxe2x80x9d is intended to mean that the binding free energy has a value which is higher than the binding free energy which has been chosen as the threshold value, meaning that the xcex94G is numerically higher than the threshold value selected. Or in other words: The term is intended to mean that the binding between the substance and the chaperone is more favourable energetically than the situation were the substance and the chaperone are suspended independently in solution.
In order to predict the binding energy in the above-indicated method, according to the invention it is especially preferred to use the following method:
Assessing the average energy difference,  less than xcex94VXxe2x88x92sel greater than , defined as  less than VXxe2x88x92sel greater than Bxe2x88x92 less than VXxe2x88x92sel greater than A, between the contribution from polar interactions to the potential energy between the chemical substance X and its surroundings (denoted s) in two states, one state (A) being where the chemical substance is surrounded by solvent, the other state (B) being where the chemical substance, bound to a periplasmic molecular chaperone or an analogue thereof, is surrounded by solvent, assessing the average energy difference,  less than xcex94VXxe2x88x92svdw greater than , defined as  less than VXxe2x88x92svdw less than Bxe2x88x92 less than VXxe2x88x92svdw greater than A, between the contribution from non-polar interactions to the potential energy between the chemical substance X and its surroundings (denoted s) in two states, one state (A) being where the chemical substance is surrounded by solvent, the other state (B) being where the chemical substance, bound to a periplasmic molecular chaperone or an analogue thereof, is surrounded by solvent, and
calculating the absolute binding free energy as an adjusted combination of the two above-mentioned average energy differences.
In the mathematical equations herein, the symbol  less than  greater than means molecular dynamics average. The index X-s means compound-solvent (or compound-surrounding), the letter xe2x80x9cXxe2x80x9d denoting the chemical substance X. Normally the substance X will function as an inhibitor of the binding between the periplasmic chaperone and pilus subunits, but as discussed herein, it is also a possibility that the compound or drug will affect the chaperone in such a way that the binding between pilus subunits and the chaperone is enhanced. The superscript xe2x80x9celxe2x80x9d designates the polar or electrostatic energy, while the superscript xe2x80x9cvdwxe2x80x9d indicates xe2x80x9cvan der Waalsxe2x80x9d, another designation for the non-polar interactions. The symbol xcex94 indicates that the quantity in state A is subtracted from the quantity in state B.
In the present context the term xe2x80x9can analogue of a periplasmic molecular chaperone,xe2x80x9d should be understood, in a broad sense, any substance which mimics (with respect to binding characteristics) an interesting-part of a periplasmic molecular chaperone (e.g. the pilus subunit binding part(s)), and the interaction of which with a chemical substance or a group or plurality of chemical substances, e.g. drug candidates, is to be studied. Thus, the analogue may simply be any other chemical compound regarded as capable of interacting with the chemical substance in a manner which mimics the binding between the chaperone and a pilus subunit in vivo, but most often the analogue will be a relatively large molecule, in other words a macromolecule such as a protein or an oligonucleotide, which is relatively large compared to the chemical substance; although the chemical substance interacting with the analogue, of course, in itself be a macromolecule. In the present context, the periplasmic molecular chaperone or analogue thereof is preferably the periplasmic chaperone or an analogue thereof which exhibits at least one interesting binding characteristic relevant for the assembly of pili.
The basis for the above-indicated approach for determining the binding free energy is explained in the following:
As a starting point is taken the linear response approximation for electrostatic forces which for polar solutions as a result yields quadratic free energy functions in response to the development of charges. This is, e.g., the familiar result from Marcus"" theory of electron transfer reactions (Marcus, 1964). For a system with two states, A and B, given by two potential energy functions VA and VB one obtains, within the approximation of harmonic free energy functions of equal curvature, the relationship (see Lee et al., 1992 and references therein):
xcex= less than VBxe2x88x92VA greater than Axe2x88x92xcex94GAB= less than VAxe2x88x92VB greater than B+xcex94GABxe2x80x83xe2x80x83(a)
where xcex94GAB is the free energy difference between B and A, xcex the corresponding reorganisation energy and  less than  greater than i denotes an average evaluated near the minimum of the potential i. Thus,
xcex94GAB≅xc2xd( less than xcex94V greater than A+ less than xcex94V greater than B)xe2x80x83xe2x80x83(b)
where xcex94V now denotes the energy difference VBxe2x88x92VA. If the hydration of a single ion is considered, this can be shown to give xcex94Gsolel=xc2xd less than VXxe2x88x92sel greater than , i.e. that the electrostatic contribution to the solvation energy equals half of the corresponding ion-solvent interaction energy (Warshel and Russell, 1984; Roux et al., 1990). Returning now to the binding problem, this result may be exploited in the following manner: For each salvation process, i.e. salvation of the substance in water and inside the protein, two states are considered where the first has the substance in vacuum and a non-polar cavity (given, e.g., by Lennard-Jones potential) already made in the given environment. The second state corresponds to the intact substance surrounded by water or the solvated protein. The linear response approximation will then again give that xcex94Gbindel≅xc2xd less than VXxe2x88x92sel greater than , where VXxe2x88x92sel is the solute-solvent electrostatic term. Hence, the electrostatic contribution to the binding free energy can be approximated by xcex94Gbindel≅xc2xd less than VXxe2x88x92sel greater than  (where the xcex94 now refers to the difference between protein and water) and thus obtained from two MD simulations of the solvated substance and of the substance-protein complex.
The validity of the linear response results in the case of ionic solvation has been confirmed, e.g., in the study by Roux et al. (1990). Some additional calculations were also performed on simple systems that corroborate the approximation of equation b. These tests were carried out by comparing the free energy obtained from FEP/MD simulations of charging Na+ and Ca2+ ions in a spherical water system ({dot over (A)}qvist, 1990) with the corresponding  less than VXxe2x88x92sel greater than  from 75 ps MD trajectories. This yielded factors relating  less than VXxe2x88x92sel greater than  to xcex94Gsolel of 0.49 for Na+ and 0.52 for Ca2+, both values being close to the predicted result of xc2xd. A similar test on the charging of a methanol molecule, given by the OPLS potential (Jorgensen, 1986) in water gave a xcex94Gsolel/ less than VXxe2x88x92sel greater than  ratio of 0.43.
A crucial question is how to account for the contribution of non-polar interactions and hydrophobic effects to the free energy of binding which was termed xcex94Gbingvdw. In the ideal case, it should be possible to estimate this contribution from the non-polar (or van der Waals) interaction energies. The liquid theories of Chandler and coworkers (Chandler et al., 1983; Pratt and Chandler, 1977) have been successfully used to analyze hydrophobic effects and to calculate free energies of transfer for some non-polar molecules (Pratt and Chandler, 1977), but no analytical treatment of that kind seems possible for salvation in an inhomogeneous environment such as a protein""s active site. However, it has been noted that the experimental free energy of salvation for various hydrocarbon compounds, such as n-alkanes, depends approximately linearly on the length of the carbon chain both in their own liquids as well as in water (Ben-Naim and Marcus, 1984). MD simulations of n-alkanes solvated in water and in a non-polar van der Waals solvent have been carried out, which indicate that also the average solute-solvent interaction energies vary approximately linearly with the number of carbons in the chain (the relationships being different in different solvents, of course). It thus seem possible that a simple linear approximation of xcex94Gbindvdw from  less than xcex94VXxe2x88x92svdw greater than  might be able to account for the non-polar binding contribution. For instance, if "sgr" is considered some appropriate measure of the size of the solute and if the solute-solvent van der Waals interaction energies and the corresponding non-polar free energy contributions (both in water and protein) depend linearly on "sgr", such that
 less than Vpvdw greater than =xcex1p"sgr",  less than Vwvdw greater than =xcex1w"sgr", xcex94Gpvdw=xcex2p"sgr"
and
xcex94Gwvdw=xcex2w"sgr"
then       Δ    ⁢          xe2x80x83        ⁢          G      bind      vdw        =                              β          p                -                  β          w                                      α          p                -                  α          w                       less than           Δ      ⁢              xe2x80x83            ⁢              V                  X          -          s                vdw               greater than   
is obtained. Since it seems difficult to derive a factor relating the two quantities in a reliable way from purely theoretical considerations, the approach is taken to empirically try to determine such a relationship which is capable of reproducing experimental binding data. Thus, the free energy of binding is in one embodiment of the invention approximated by
xcex94Gbind=xc2xd less than xcex94VXxe2x88x92sel greater than +xcex1 less than xcex94VXxe2x88x92svdw greater than xe2x80x83xe2x80x83(1)
the parameter xcex1 being determined by empirical calibration.
Although, as discussed above, a theoretical prediction of the coefficient for  less than xcex94VXxe2x88x92sel greater than  is xc2xd, it may be practically useful to also treat this coefficient as an empirical parameter. This would lead to the free energy of binding being approximated by
xcex94Gbind=xcex2 less than xcex94VXxe2x88x92sel greater than +xcex1 less than xcex94VXxe2x88x92svdw greater than xe2x80x83xe2x80x83(1b)
where both parameters, xcex1 and xcex2, are determined by empirical calibration.
Finally, in some cases, it seems suitable to add an additional constant term to Equation 1, so that the equation becomes
xcex94Gbind=xc2xd less than xcex94VXxe2x88x92sel greater than +xcex1 less than xcex94VXxe2x88x92svdw greater than +cxe2x80x83xe2x80x83(2)
where c is a constant reflecting extrapolation to zero size of the chemical substance, that is, where the regression line is distinctly offset from origin when moving towards zero size of the chemical substance. The parameter c may also be used to correct for possible systematic errors due to e.g. the neglect of induced polarisation, possible force field deficiencies etc. In these cases, c will normally assume a value between xe2x88x9210 and 10 kcal/mol, typically between xe2x88x923 and 3 kcal/mol, such as between xe2x88x922 and 2 kcal/mol, e.g. between xe2x88x921 and 1 kcal/mol. However, it is anticipated that in many cases, c can suitably be set to zero, as the extent of deviation will be of minor importance for the usefulness of the predicted values.
If also the electrostatic coefficient i treated as an empirical parameter, the approximation of the binding free energy assumes its most general form, namely
xcex94Gbind=xcex2 less than xcex94VXxe2x88x92sel greater than +xcex1 less than xcex94VXxe2x88x92svdw greater than +cxe2x80x83xe2x80x83(2b)
where now both xcex1, xcex2 and c are to be determined by empirical calibration.
While the solvent used in the above method is suitably and most often an aqueous solvent like water, it is within the scope of the invention to take any other suitable solvent as a starting point, including, e.g., methanol, ethanol, acetone, acetonitrile, chloroform, hexane, etc., or mixtures thereof or combinations of such solvents or mixtures thereof with water. The selection of the solvent will be of little importance to the predicted values as long as the solvent is one which is able to dissolve or solvate the receptor molecule and the substance (in the present context this means that a sufficient amount of the periplasmic molecular chaperone or analogue thereof can be homogeneously mixed with the solvent without precipitation so as to allow the determination of binding energies by some suitable method), but there may be cases where it is advantageous to modify the solvent environment (e.g. by modulating the ionic strength) in which the interaction of the substance and the receptor molecule is to take place. If the environment in which the interaction between the chemical substance, such as a drug, and a periplasmic molecular chaperone or an analogue thereof is to take place in the actual use of the drug is the human body, it might be particularly suitable to imitate e.g. human plasma as the solvent.
A thorough discussion of the above-referenced method for determining the binding free energy between two molecules can be found in International Patent Application No. PCT/IB94/00257 and in {dot over (A)}qvist et al, 1994. These two documents are hereby incorporated by reference.
The above referenced method for determining the binding free energy has been employed in example 3 in order to identify compounds which stands a high chance of binding to the binding site of PapD; this means that calculations as the above described have been performed as the last theoretical step before compounds have actually been synthesized.
It will be understood that the above mentioned methods for identifying substances capable of interacting with chaperones will prove especially efficient in identifying substances which are of potential pharmaceutical value if the site to which they bind is known to be involved in pilus assembly.
Therefore, it is preferred that the site with which the substance may potentially interact, and to which the binding free energy is predicted, is the pilus subunit binding part of a molecular chaperone, such as the pilus subunit binding site of a molecular chaperone selected from the group consisting of PapD, FimC, SfaE, FaeE, FanE, Cs3-27, F17D, ClpE, EcpD, Mrkb, FimB, SefB, HifB, MyfB, PsaB, PefD, YehC, MrpD, CssC, NfaE, AggD and Caf1M, or an analogue of such a pilus subunit binding site, since the pilus subunit binding sites in these chaperones show extensive homologies. It is especially preferred that the binding site is the pilus subunit binding site of PapD or an analogue thereof.
As will appear from the examples, an important part of the chaperone binding motif has been discovered and a peptide corresponding to this motif has been synthesized and co-crystallized with PapD to provide a structural basis for the mechanism of action of PapD. The molecular details of the PapD-adhesin recognition interface clearly demonstrate the function of the conserved cleft in the entire pilus chaperone superfamily in subunit binding and in shuttling virulence determinants to the surface of pathogenic bacteria. The PapD-peptide crystal structure essentially represents a xe2x80x9csnapshotxe2x80x9d of a fundamental process in bacterial pathogenesis: the interaction of an adhesin with a chaperone, which is a prerequisite to adhesin presentation on the microbial surface.
Thus, the inventors of the present invention have by the use of X-ray crystallography elucidated the mechanism of binding between PapD and the pilus subunit PapG thereby identifying an essential part of a defined binding site responsible for the binding between pilus subunits and their periplasmatic chaperones, and thus providing a method to enable drug design of chaperone inhibiting anti-bacterial compounds.
Having determined the location of a promising binding site for inhibitory ligands as described above (see details in examples 1 and 2), the computer programs xe2x80x9cPLIMxe2x80x9d and xe2x80x9cPLIM_DBSxe2x80x9d (developed by Symbicom AB) have been used to find templates for families of compounds capable of binding to the binding site.
PLIM is a Protein Ligand Interaction Modeller that constructs putative ligands for a protein using thermodynamic criteria. It calculates the energy of interaction between the protein and sample probes that are successively placed at different points on a regular grid around the molecule. For each position and orientation the interaction energy between the probe and the atoms of the protein is calculated. The energies are stored, and the best positions for a particular probe are written out (the basic calculations are described by Goodford (1985) and Boobbyer (1989) and implemented in the commercially available program GRID; the PLIM implementation is somewhat different in that the energy values are converted to discrete points that are associated with the chemical probe, enabling easy output to e.g. data base searching programs). The program then builds up the ligand by incorporating selected probe atoms at positions of energy minima on the grid. The user selects which atoms and groups should be used as probes, and which criteria should be used to determine those that will be incorporated into the ligand. The energy is calculated as the sum of electrostatic, Van der Waals and hydrogen-bonding contributions as described herein.
The PLIM runs result in a number of suggested positions and orientations of favourable chemical groups in the region near the binding site. These groups which have physical properties like charge, hydrogen bonding directionality and extended atom radia, will hereafter be denoted xe2x80x9csite pointsxe2x80x9d.
A search for potential ligands is then made by searching a database for known molecular structures that match the positions of these groups of site points, using PLIM_DBS.
The core of PLIM_DBS is an algorithm for subgraph isomorphism (cf. Ullman (1976) and Brint (1987)), where three sitepoints are represented as a distance matrix (xe2x80x9cthe pattern matrixxe2x80x9d). The program looks for this distance pattern in the distance matrix formed from every entry in the database. If the pattern is found, the entry is superimposed on to the sitepoints and if the corresponding atom types match the entry and its orientation is saved in a hit-list. Added to this basic scheme a number of options regarding surface complementarity can be used, i.e. only entries which are matching the protein surface with respect to hydrophobic and steric properties are saved.
PLIM_DBS is thus a database searcher which hunts through a collection of 3-dimensional molecule coordinate sets, looking for entries that contain a certain pattern of atoms. This pattern is specified in terms of atom type, and of spatial position and orientation; for instance a search may be made for compounds containing an sp3 carbon atom that is 4.2 xc3x85 from a sp2 oxygen and 5.1 xc3x85 from a hydroxyl group that in turn is 5.6 xc3x85 from the oxygen. The strictness of the search can be adjusted by the user by varying the tolerance on the distance criteria and the atom-type matching, determining, for instance, whether a sp2 carbon that is a little more than 4.2 xc3x85 from an oxygen should be considered as a hit. Those hits that are found are then ranked according to a score that reflects how well the target atoms superimpose on the real molecule, and also on how complementary the molecular surface of the compound is to that of the binding pocket of the protein.
The result from a PLIM_DBS search is a list of molecular structures and their atomic coordinates, superpositioned on to the sitepoints, and given a score (xe2x80x9cgoodness of fitxe2x80x9d).
The procedure does not try to optimize the positioning of the structures, nor does it perform any molecular mechanics or dynamics calculations. Both protein and the extracted structures are treated as rigid bodies.
The structures from the database search are displayed in the context of the protein and its surface on a graphics system using a commonly available molecular modelling package. Usually the structures show some unfavourable interactions with the protein, or lack groups to fill out e.g. hydrophobic pockets. Hence, the structures form the database search are regarded as templates, to be modified and improved by an organic chemist. This process also involves choosing compounds which are easy to synthesize, which is of particular interest if the synthesis capacity is limited.
The best of these database hits are thus examined visually using a computer-graphic modelling system, and the most promising of these are selected according to a wealth of physico-chemical reasoning.
The templates are modified using a small molecule 3D builder (MacMimic). Each template gives rise to a compound class, e.g. denoted xe2x80x9chdoxe2x80x9d. Each modification assigned a specific number (e.g. hdoxe2x80x943) and the coordinates and a description are stored in a tree structure, using the program ARVS_JAKT developed by Symbicom. The design is performed in a collaboration between protein structure experts and organic chemists, in order to provide the best tools possible for the chemists who will actually synthesize the compounds.
The efficacy of these modifications is finally assessed using molecular-dynamics free energy calculations as described herein to study the stability of the protein-ligand complex ({dot over (A)}qvist et al., 1994; {dot over (A)}qvist and Medina, 1993).
In order to maximize the efficiency of the above-mentioned methods for identifying/designing substances which are capable of interacting with a molecular chaperone, it is preferred that the substance A is likely to be a substance which is capable of binding to the selected binding site.
In view of the above-described modus operandi for selecting substances which should interact with chaperones like PapD, this can, according to the invention, be accomplished when the substance A is selected by performing the following steps:
co-crystallizing the periplasmic molecular chaperone or the analogue thereof with a ligand capable of interacting with a site in the periplasmic molecular chaperone or the analogue thereof and establishing the three-dimensional conformation of the periplasmic molecular chaperone or the analogue thereof and the ligand when interacting by means of X-ray crystallography,
using the above-established conformation of the periplasmic molecular chaperone or the analogue thereof to establish a 3-dimensional representation of the site in the periplasmic molecular chaperone or the analogue thereof interacting with the ligand during binding,
selecting a number of distinct chemical groups, X1, and determining the possible spatial distributions of the X1 chemical groups which maximizes the binding free energy between the chemical groups and the site in the chaperone or the analogue interacting with the ligand,
extracting, from a database comprising three-dimensional representations of molecules, a molecule which has the X1 chemical groups in the possible spatial distributions determined above,
optionally modifying the 3-dimensional representation of the molecule extracted from the database, and identifying the optionally modified molecule as the substance A.
According to the invention the above-indicated steps are especially preferred when the ligand is a pilus subunit or a part thereof with which the chaperone normally interacts during transport of the pilus subunit through the periplasmic space and/or during pilus assembly.
By the use of the above-mentioned method for identifying substances capable of interacting with the periplasmic chaperones, several classes of substances have been identified which have proved promising in tie design phase.
Drug design efforts for inhibitors/enhancers to PapD have concentrated on the region of the molecule where the G-peptide is observed to bind. This region will now be described in detail, using one of the putative inhibitors (bpyxe2x80x949, see below) as a reference structure.
The binding site is dominated by the central charged side chains of Arg-8 and Lys-112, which bind to the sulphate moiety of bpyxe2x80x949. Adjacent to this is a small, shallow hydrophobic pocket formed by the side-chains of Ile-154, Ile-194, and Thr-7, against which the 2-ethyl group of bpyxe2x80x949 packs (Pocket 1). A group as large as a phenyl ring could be accommodated here, attached to sugar position 2, and with possible substituents that could receive or donate a hydrogen bond to Thr-7, or donate to the backbone carbonyl of 198.
There is also a larger pocket comprising residues Leu-4, Ile-111, Thr-7 and Thr-109, in which the phenyl ring of bpyxe2x80x949 nestles (Pocket 2). A group as large as naphthalene could be substituted on the 6-position of the carbohydrate scaffold to fill this sub-site, with substituents that could form a hydrogen bond to Thr-109, or to any of the polar backbone atoms of residues Leu-4, Arg-6, or Lys-110. Then there is a long, shallow patch that includes Tyr-87, and the aliphatic regions of Lys-110 and Lys-112, which could accommodate a tricyclic system such as 2-phenanthryl substituted on position 3 of the sugar (Patch 3). Substituents to hydrogen bond to Tyr-87 or the backbone of Lys-110 can be considered, as well as negatively charged groups to complement the side chains of Lys-110 and Lys-112. Tyr-87 is a potential charge-transfer donor to a electron deficient xcfx80-system such as a nitroaryl.
Models of several homologous chaperones (SfaE, MrkB, HifB and FimC) have been made from the PapD structure, and differences between the model structures has influenced the design of inhibitors, such that proposed ligands should bind to all the structures looked at. For example, it is tempting to complement the charged side chain of Arg-200 with an acidic group in the ligand, but since two of the other structures have an Asp at this position, the residue is not considered as a good candidate. Arg-8 is fully conserved, as is Lys-112, Thr-7 and Ile-11. Tyr-87 becomes a Trp in three structures, but the overall nature of patch 3 is not changed by this. PapD is actually alone with its Thr-Lys sequence at 109-110, all of the four other structures being Ser-Arg here, but again, these conservative changes do not significantly alter design criteria.
Although substances which interact with the binding site responsible for binding to G-proteins are obvious candidates as inhibitors/enhancers of periplasmic chaperones, it will be understood that molecules capable of interacting with other sites in periplasmic chaperones are interesting in this aspect, too. It is highly possible that an interaction with another site than the one binding G-protein in i.e. PapD may cause PapD to either be prevented, inhibited or enhanced in its action as a periplasmic chaperone.
As mentioned above, a family of substances (called the bpy family herein) is an important aspect of the invention. Thus, the invention relates to novel compounds of the general formula: 
wherein
V1 is O, S, SO, SO2, CH2, C(OH)H, CO or CS;
W1 is O, S, SO2, SO3, CH2 or NH;
R1 is H; C1-24 alkyl, C1-24 alkenyl or C1-24 alkynyl, which alkyl, alkenyl and alkynyl may be substituted with one or more substituents independently selected from OH, xe2x80x94CONH2, xe2x80x94CSNH2, xe2x80x94CONHOH, xe2x80x94CSNHOH, xe2x80x94NHCHO, xe2x80x94NHCONH2, xe2x80x94NHCSNH2, xe2x80x94NHSO2NH2 and xe2x80x94SO2NH2; acyl; or xe2x80x94(CH2CH2O)sxe2x80x94H, wherein s=1,2,3;
R2 is a group of the formula 
wherein
A is xe2x80x94CHxe2x80x94(CH2)nxe2x80x94, or xe2x80x94CHxe2x95x90CHxe2x80x94(CH2)nxe2x88x921xe2x80x94(n greater than 0) or 
B is xe2x80x94(CH2)mxe2x80x94 or xe2x95x90CHxe2x80x94(CH2)mxe2x88x921xe2x80x94 (m greater than 0);
X2 is N, CH or C (when B is xe2x95x90CHxe2x80x94(CH2)mxe2x88x921xe2x80x94; and
Y2 is O, S, NH, H2 or H (n=1); and
4 greater than m+n greater than 0, n less than 3, and m less than 3;
or R2 is a group of the formula 
wherein
A is xe2x80x94CHxe2x80x94(CH2)nxe2x80x94, or xe2x80x94CHxe2x95x90CHxe2x80x94(CH2)nxe2x88x921xe2x80x94 (n greater than 0) or 
B is xe2x80x94(CH2)mxe2x80x94 or xe2x95x90CHxe2x80x94(CH2)mxe2x88x921xe2x80x94 (m greater than 0); and
Xxe2x80x22 is O, NH, CH2 or S (when p=0); N or CHxe2x80x94 (p=1);
or C (when p=1 and B is xe2x95x90CHxe2x80x94(CH2)mxe2x88x921xe2x80x94);
V2, Z2 and W2 are independently H, OH, xe2x80x94CONH2, xe2x80x94CSNH2, xe2x80x94CONHOH, xe2x80x94CSNHOH, xe2x80x94NHCHO, xe2x80x94NHCONH2, xe2x80x94NHCSNH2, xe2x80x94NHSO2NH2, xe2x80x94SO2NH2, or V2 and Z2, or Z2 and W2 together form xe2x80x94NHC(O)NHxe2x80x94, xe2x80x94C(O)NHC(O)xe2x80x94, xe2x80x94NHS(O2)NHxe2x80x94, xe2x80x94C(O)NHOxe2x80x94, xe2x80x94C(S)NHOxe2x80x94, xe2x80x94S(O2)NHOxe2x80x94, or xe2x80x94S (O2)NHC (O)xe2x80x94;
4 greater than m+n greater than 0, n less than 3, and m less than 3;
or R2 is a group xe2x80x94W5xe2x80x94(C1-5 alkyl or C2-5 alkenyl or C2-5 alkynyl) wherein W5 is a bond or is selected from xe2x80x94Oxe2x80x94, xe2x80x94Sxe2x80x94, xe2x80x94SO2xe2x80x94, and xe2x80x94NHC(O)xe2x80x94, and the C1-5 alkyl, C2-5 alkenyl or C2-5 alkynyl moiety may be substituted with up to three groups selected independently from OH, xe2x80x94CONH2, xe2x80x94CSNH2, xe2x80x94CONHOH, xe2x80x94CSNHOH, xe2x80x94NHCHO, xe2x80x94NHCONH2, xe2x80x94NHCSNH2, xe2x80x94NHSO2NH2 and xe2x80x94SO2NH2;
xe2x80x94Z1xe2x80x94R3 is xe2x80x94SO2(OH), xe2x80x94PO(OH)2, xe2x80x94OSO2(OH), xe2x80x94NHSO2(OH), xe2x80x94NHxe2x80x94COxe2x80x94COOH, xe2x80x94SPO(OH)2, xe2x80x94CH2COOH, tetrazol-5-yl or tetrazol-5-ylmethyl, or salts thereof;
or Z1 is xe2x80x94Oxe2x80x94, xe2x80x94Sxe2x80x94, xe2x80x94NHxe2x80x94, or xe2x80x94CH2xe2x80x94, and R3 is a group of the formula: 
D is xe2x80x94CH2xe2x80x94, xe2x80x94COxe2x80x94, xe2x80x94SO2xe2x80x94, xe2x80x94NHxe2x80x94SO2xe2x80x94, xe2x80x94NHxe2x80x94COxe2x80x94, xe2x80x94Oxe2x80x94PO(OH)xe2x80x94 or a salt thereof;
Z3 is H, OH, xe2x80x94CONH2, xe2x80x94CSNH2, xe2x80x94CONHOH, xe2x80x94CSNHOH, xe2x80x94NHCHO, xe2x80x94NHCONH2, xe2x80x94NHCSNH2, xe2x80x94NHSO2NH2xe2x80x94, xe2x80x94SO2NH2, xe2x80x94SO2(OH), xe2x80x94PO(OH)2, xe2x80x94OSO2(OH), xe2x80x94NHSO2(OH), xe2x80x94COOH, tetrazolyl-5-yl or tetrazolyl-5-ylmethyl or a salt thereof,
with the proviso that when D is xe2x80x94CH2xe2x80x94, xe2x80x94COxe2x80x94, xe2x80x94SO2xe2x80x94, xe2x80x94NHSO2xe2x80x94 or xe2x80x94NHCOxe2x80x94, then Z3 is xe2x80x94SO2(OH), xe2x80x94PO(OH)2, xe2x80x94OSO2(OH), xe2x80x94NHSO2(OH), xe2x80x94COOH, tetrazolyl-5-yl or tetrazolyl-5-ylmethyl or a salt thereof;
X3 and Y3 independently are H, NO2, SO2NH2, CONH2, CF3 or F; and
U4-W4 is xe2x80x94CHCHxe2x80x94, xe2x80x94CH2CH2xe2x80x94, xe2x80x94C(OH)CHxe2x80x94, xe2x80x94CHC(OH)xe2x80x94, xe2x80x94CH(OH)CH2xe2x80x94, xe2x80x94CH2CH(OH)xe2x80x94, xe2x80x94CH(OH)CH(OH)xe2x80x94, xe2x80x94C(O)NHxe2x80x94, xe2x80x94NHC(O)xe2x80x94;
Y1 is xe2x80x94Oxe2x80x94 or xe2x80x94Sxe2x80x94;
R4 is H or, when Y1 is S, S (CH2)qN(R9)3+ and q is an integer 2-4, where R9 H or C3;
R5 is H; C1-6 alkyl, C2-6 alkenyl or C2-6 alkynyl, and the C1-6 alkyl, C2-6 alkenyl or C2-6 alkynyl moiety may be substituted with OH, xe2x80x94CONH2, xe2x80x94CSNH2, xe2x80x94CONHOH, xe2x80x94CSNHOH, xe2x80x94NHCHO, xe2x80x94NHCONH2, xe2x80x94NHCSNH2, NHSO2NH2 or xe2x80x94SO2NH2; or aryl, aryl(C1-2)alkyl, heterocyclyl, or heterocyclyl(C1-2)alkyl which may optionally be substituted in the aryl or heterocyclyl moieties with one, two or three substituents selected independently from OH, F, Cl, NH2, CONH2, NHCOH, and SO2NH2;
X1 is xe2x80x94Oxe2x80x94, xe2x80x94Sxe2x80x94or xe2x80x94NHxe2x80x94;
R6 is H or, when X1 is NH, acyl, HOCNH-Val-Met-, HOCNH-Ile-(S,S)-dioxo-methionyl- or HOCNH-Val-(pyran-4-on-2-yl)-ala-nyl-;
or a salt of such a compound.
Another family of substances called the hdo-family has also been synthesized. Hence, the invention also relates to novel compounds of the general formula 
wherein
X is O, P, P(O), S, SO, SO2, CH2, C(OH)H, or a group NQ11, wherein Q11 is H, OH, C1-24 acyl or C1-24 alkyl;
Z11 is a bond, O, CH2, S, SO, SO2, or a group NQ12, wherein Q12 is H, C1-24 acyl or C1-24 alkyl;
R11 is H; C1-24 alkyl, C2-24 alkenyl, or C2-24 alkynyl, which may be substituted with one or more substituents independently selected from xe2x80x94OH, xe2x80x94COOH, xe2x80x94F, xe2x80x94Cl, xe2x80x94CONH2, xe2x80x94CSNH2, xe2x80x94CONHOH, xe2x80x94CSNHOH, xe2x80x94NHCHO, xe2x80x94NHCONH2, xe2x80x94NHCSNH2, xe2x80x94NHSO3NH2 and xe2x80x94SO2NH2; acyl; or xe2x80x94(CH2CH2O)sxe2x80x94H, wherein s=1, 2, or 3;
or R11 is CHxe2x95x90CHxe2x80x94(CH2)nxe2x80x2xe2x80x94Q13 or xe2x80x94(CH2)nxe2x80x2xe2x80x94Q13, wherein Q13 is an aryl or a heteroaryl group substituted with xe2x80x94OH, xe2x80x94COOH, xe2x80x94F, xe2x80x94Cl, xe2x80x94CONH2, xe2x80x94CSNH2, xe2x80x94CONHOH, xe2x80x94CSNHOH, xe2x80x94NHCHO, xe2x80x94NHCONH2, xe2x80x94NHCSNH2, xe2x80x94NHSO3NH2 and xe2x80x94SO2NH2, and wherein nxe2x80x2xe2x89xa70;
R12 and R13 are independently OH, H, F, Cl, OW11, or O(CO)W11, wherein W11 is C1-24 alkyl, C2-24 alkenyl or C2-24 alkynyl, or an aryl or a heteroaryl group substituted with xe2x80x94OH, xe2x80x94COOH, xe2x80x94F, xe2x80x94Cl, xe2x80x94CONH2, xe2x80x94CSNH2, xe2x80x94CONHOH, xe2x80x94CSNHOH, xe2x80x94NHCHO, xe2x80x94NHCONH2, xe2x80x94NHCSNH2, xe2x80x94NHSO3NH2 and xe2x80x94SO2NH2;
Z12 is a bond, O, S, or CH2;
R14 is xe2x80x94(CH2)nxe2x80x3xe2x80x94Q14, wherein Q14 is an aryl group or a heteroaryl group substituted with xe2x80x94OH, xe2x80x94COOH, xe2x80x94F, xe2x80x94Cl, xe2x80x94CONH2, xe2x80x94CSNH2, xe2x80x94CONHOH, xe2x80x94CSNHOH, xe2x80x94NHCHO, xe2x80x94NHCONH2, xe2x80x94NHCSNH2, xe2x80x94NHSO3NH2 and xe2x80x94SO2NH2, and wherein nxe2x80x3=0, 1, 2, or 3;
Z13 is a bond, O, CH2, S, SO, SO2, NQ14Q15, wherein Q14 is H, C1-24 acyl or C1-24 alkyl, and Q15 is CO or xe2x80x94C(O)W12, wherein W12 is O or NW13, wherein W13 is H, OH, C1-24 acyl or C1-24 alkyl;
R15 is H; C1-24 alkyl, C2-24 alkenyl or C2-24 alkynyl, which alkyl, alkenyl and alkynyl may be substituted with one or more substituents independently selected from, xe2x80x94OH, xe2x80x94COOH, xe2x80x94F, xe2x80x94Cl, xe2x80x94CONH2, xe2x80x94CSNH2, xe2x80x94CONHOH, xe2x80x94CSNHOH, xe2x80x94NHCHO, xe2x80x94NHCONH2, xe2x80x94NHCSNH2, xe2x80x94NHSO3NH2 and xe2x80x94SO2NH2; acyl or xe2x80x94(CH2CH2O)sxe2x80x94H, wherein s=1, 2, or 3;
or R15 is CHxe2x95x90CHxe2x80x94(CH2)nxe2x80x2xe2x80x94Q13, or xe2x80x94(CH2)nxe2x80x2xe2x80x94Q13, wherein Q3 is as defined above and wherein nxe2x80x2xe2x89xa70;
or a salt of such a compound.
In the present context, the terms xe2x80x9cC1-5, C1-6 and C1-24 alkylxe2x80x9d is intended to mean alkyl groups with 1-5, 1-6 and 1-24 carbon atoms, respectively, which may be straight or branched or cyclic such as methyl, ethyl, propyl, isopropyl, butyl, isobutyl, tert.butyl, hexyl, octyl, dodecyl, cyclopentyl, cyclohexyl, etc.
Further, as used herein, the terms xe2x80x9cC2-5, C2-6 and C2-24 alkenylxe2x80x9d is intended to mean mono- or polyunsaturated alkyl; groups with 2-5 and 2-24 carbon atoms, respectively, which may be straight or branched or cyclic in which the double bond(s) may be present anywhere in the chain or the ring, for example vinyl, 1-propenyl, 2-propenyl, hexenyl, decenyl, 1,3-heptadienyl, cyclohexenyl etc. Some of the substituents exist both in a cis and a trans configuration. The scope of this inventions comprises both the cis and trans forms.
In the present context, the terms xe2x80x9cC2-5, C2-6 and C2-24 alkynylxe2x80x9d is intended to mean a straight or branched alkyl group with 2-5 and 2-24 carbon atoms, respectively, and incorporating one or more triple bond(s), e.g. ethynyl, 1-propynyl, 2-propynyl, 2-butynyl, 1,6-heptadiynyl, etc.
The terms xe2x80x9cC1-6 and C1-24 alkoxyxe2x80x9d designate alkyl groups as defined above comprising an oxy function.
In the present context, the term xe2x80x9carylxe2x80x9d is intended to mean phenyl and naphthyl. The term xe2x80x9cheteroarylxe2x80x9d is intended to mean a cyclic aromatic system, wherein at least one non-carbon atom contributes to the xcfx80 bonding system.
Examples of substituted aryl groups are: 3-nitrophenyl, 3-hydroxyphenyl, 4-hydroxyphenyl, 3,4-dihydroxyphenyl, 3-carboxamidophenyl, 3-formamidylphenyl, 3-acetamidylphenyl, 3-fluoronaptht-2-yl, 7-fluoronaphthyl, 3,7-difluoronaphthyl, 3-hydroxynaphthyl, 7-hydronaphthyl, 3,7-dihydroxynaphthyl, 3-fluoro-7-hydroxynaphthyl, 7-fluoro-3-hydroxynaphthyl, 4-fluoronaphth-2-yl, 6-fluoronaphth-yl, 8-fluoronaphth-2-yl, 4,6-difluoronaphth-2-yl etc.
Examples of heterocyclic and heteroaryl groups are pyrrolyl, furanyl, 2,3-dihydrofuranyl, tetrahydrofuranyl, thienyl, 2,3-dihydrothienyl, tetrahydrothienyl, imidazolyl, oxazolyl, thiazolyl, pyrazolyl, indolyl, pyrazinyl, dioxolanyl, dioxanyl, 1,3,5-trioxanyl, tetrahydrothiapyranyl, dithiolanyl, pyrazolidinyl, iminazolidinyl, sym-triazinyl, sym-tetrazinyl, quinazolinyl, pteridinyl, isoindolyl, 1,2,4-triazolyl, 1,2,3-triazolyl, benzimidazolyl, indazolyl, benzofuranyl, isobenzofuranyl, benzothiophenyl, thienothiophenyl, isoxazolyl, 1,2,5-oxadiazolyl, isothiazolyl, 1,3,4-thiadiazolyl, benzoxazolyl, benzothiazolyl, azaindolyl, oxoindolyl, hydroxyindolyl, N-oxyisoquinolyl etc.
In the present context, the term xe2x80x9cacylxe2x80x9d (e.g. C1-24 acyl) is intended to designate the acyl residue of a carboxylic acid or a sulphonic acid moiety comprising a carbonyl or sulphonyl group and an organic moiety. Examples of acyl groups include C1-24 alkanoyl (e.g. formyl, acetyl, propionyl, butyryl, isobutyryl, valeryl, isovaleryl, pivaloyl and hexanoyl), C1-24 alkenoyl (e.g. acryloyl, metacryloyl, crotonoyl, isocrotonoyl, 2-pentenoyl, 3-pentenoyl, 2-methylpentenoyl, 3-pentenoyl, 3-phenylpropenoyl, 2-phenyl-trans-propenoyl, 2,4-hexadienoyl), C1-24 alkynoyl (e.g. propyonyl, 2-butynoyl, 3-butynoyl, 2-methyl-3-butynoyl, 2,2-dimethylbutynoyl, 2-pentynoyl, 3-pentynoyl, 2-pentyn-4-trans-enoyl), C1-24 alkoxycarbonyl (e.g. methoxycarbonyl, ethoxycarbonyl, propoxycarbonyl, butoxycarbonyl and t-butoxycarbonyl), C1-24 alkenyloxycarbonyl (e.g. cis-2-butenyloxycarbonyl, 1-methyl-2-propenyloxycarbonyl, 1,1-dimethyl-2-propenyloxycarbonyl, trans-2-butenyloxycarbonyl), aroyl (e.g. benzoyl), heterocyclylcarbonyl (e.g. 2-furoyl, 3-furoyl, 2-furanoyl, 3-furanoyl,-2-pyrrolcarboxyl, 3-pyrrolcarboxyl, 2-thenoyl, 3-thenoyl, 2-indolcarboxyl, 3-indolcarboxyl, 1-naphthanoyl and 2-naphthanoyl), etc.
The term xe2x80x9csaltxe2x80x9d is intended to comprise a salt such as an organic acid addition salt (e.g. acetate, valerate, salicylate, galacturonate, gluconate, tannate, triflouroacetate, maleate, tartrate, methanesulfonate, benzenesulfonate, formiate, thiocyanate and toluenesulfonate), an inorganic acid addition salt (e.g. hydrochloride, hydrobromide, hydroiodide, dihydrochloride, dihydrobromide, dihydroiodide, sulphate, hydrogensulphate, halosulphate such as iodosulphate, nitrate, phosphate, and carbonate) or a salt with an amino acid (e.g. arginine, aspartic acid and glutamic acid) or a metal salt such as an alkali metal salt (e.g. sodium salt and potassium salt) and an earth alkali metal salt (e.g calcium salt and magnesium salt), an ammonium salt, an organic alkali salt (e.g. trimethylamine salt, triethylamine salt, pyridine salt, picoline salt, dicyclohexylamine salt and N,Nxe2x80x2-dibenzylethylenediamine salt), and hydrates thereof.
When the substituent R5 designates heterocyclyl, it is preferred that the substituent designates a heterocyclyl group of the formula 
wherein xe2x80x2X is xe2x80x94CHxe2x80x94, xe2x80x94CH2xe2x80x94, xe2x80x94Oxe2x80x94, xe2x80x94Nxe2x80x94, xe2x80x94Sxe2x80x94, xe2x80x94Sxe2x86x92O, xe2x80x94Nxe2x86x92O or xe2x80x94COxe2x80x94, Y is xe2x80x94CHxe2x80x94 or xe2x80x94NHxe2x80x94, and Z is xe2x80x94CHxe2x80x94, xe2x80x94CH2xe2x80x94, xe2x80x94Oxe2x80x94, xe2x80x94Sxe2x80x94, xe2x80x94Nxe2x80x94, xe2x80x94COxe2x80x94, xe2x80x94Sxe2x86x92O or xe2x80x94Nxe2x86x92O, especially a group selected from the group consisting of inden-7-yl, benzofuran-4-yl, isobenzofuran-4-yl, thionaphthen-4-yl, isothionaphthen-4-yl, 2-oxo-inden-7-yl, 2-oxo-inden-4-yl, inden-4-yl, benzofuran-7-yl, isobenzofuran-7-yl, thionaphten-7-yl, isothionaphthen-7-yl, 1-oxo-thionaphthen-4-yl, 1-oxo-thionaphthen-7-yl, anthran-4-yl, anthran-7-yl, thioanthran-4-yl, thioanthran-7-yl, benzthiozol-4-yl, benzthiozol-7-yl, 2H-2-isobenzo-1,3-dion-7-yl, isobenzofuran-5-yl, isobenzofuran-6-yl, 3H-2-oxo-benzofuran-5-yl, 3H-2-oxo-benzofuran-6-yl, 3H-2-oxothionaphthen-5-yl, 3H-2-oxothionaphthen-6-yl, indol-5-yl, indol-6-yl, 3H-2-oxoindol-5-yl, 3H-2-oxoindol-6-yl, 3H-2-oxobenzoxazol-5-yl, 3H-2-oxobenzoxazol-6-yl, benzothiazol-5-yl, benzothiazol-6-yl, 2-oxobenzo-1,3-dithiol-5-yl, 2-oxobenzo-1,3-dithiol-6-yl, 3H-2-oxobenzimidazol-5-yl, 3H-2-oxobenzimidazol-6-yl, benzoxathiol-5-yl, benzoxathiol-6-yl, 3H-2-oxobenzthiazol-5-yl and 3H-2-oxobenzthiozol-6-yl.
It is also preferred that the substituent R5 is a group of the formula 
or that R5 is a group of the formula 
With respect to the substituent R2 being heterocyclyl, it is especially preferred that it is selected from the group consisting of isobenzofuran-5-yl, isobenzofuran-6-yl, 3H-2-oxo-benzofuran-5-yl, 3H-2-oxo-benzofuran-6-yl, 3H-2-oxothionaphthen-5-yl, 3H-2-oxothionaphthen-6-yl, indol-5-yl, indol-6-yl, 3H-2-oxoindol-5-yl, 3H-2-oxoindol-6-yl, 3H-2-oxobenzoxazol-5-yl, 3H-2-oxobenzoxazol-6-yl, benzothiazol-5-yl, benzothiazol-6-yl, 2-oxobenzo-1,3-dithiol-5-yl, 2-oxobenzo-1,3-dithiol-6-yl, 3H-2-oxobenzimidazol-5-yl, 3H-2-oxobenzimidazol-6-yl, benzoxathiol-5-yl, benzoxathiol-6-yl, 3H-2-oxobenzthiazol-5-yl and 3H-2-oxobenzthiozol-6-yl.
The exact number of substituents present on an alkyl, alkenyl or alkynyl moiety R1 will be dependent on the length of the carbon chain, the purpose of the substituents being to cause the entire group R1 to be compatible with water since, in the chaperone-ligand-complex such as the PapD-ligand complex, the group R1 will extend into the surrounding aqueous medium. Thus, for a fairly short carbon chain such as up to four carbon atoms, it is contemplated that one of the above polar substituents will be sufficient, in particular when the substituent is located terminally whereas, for longer chains, a larger number of substituents, such as a substituent for every other carbon atom, may be required.
The 4,6-O-(4xe2x80x2-Methoxy)phenylmethylidene-xcex1-D-glucohexopyranoside or 4,6-O-(4xe2x80x2-Methoxy)phenylmethylidene-xcex2-D-glucohexopyranoside glycosides: 
(used here as preferred examples, but other arylmethylidene or vinylidene acetals may be used) can be prepared as follows: Peracylated glucose is reacted with, e.g. hydrogen bromide or hydrogen chloride in a suitable solvent such as, e.g. acetic acid or dichloromethane, to form per-O-acylated glycosyl bromide or chloride (O-acylation and glycosyl halide synthesis: M. L. Wolfrom and A. Thompson, Methods in Carbohydrate Chemistry, Vol. 2, 211-215, ed. by R. L. Whistler and L. Wolfrom, Academic Press, New York, 1963; G. Hewit and G. Fletcher Jr., ibid, 226-228; and R. U. Lemieux, ibid, 223-224)
The suitably protected, when necessary, aglycone alcohol or thiol (H-W1R1-PG1 or H-W1R1) (protecting groups: Protective Groups in Organic Synthesis, Editors T. W. Greene and P. G. M. Wuts, John Wiley and Sons, Inc., New York, 1991) is reacted with the per-O-acylated glucose using a Lewis acid such as borontrifluoride etherate (R. J. Ferrier and R. H. Furneaux, Carbohydr. Res., 52 (1976) 63-68; J. Dahmxc3xa9n, T. Frejd, G. Grxc3x6nberg, T. Lave, G. Magnusson, and G. Noori, Carbohydr. Res 116 (1983) 303-307) or trimethylsilyltrifluoromethanesulphonate (T. Ogawa, K. Beppu, S. Nakabayashi, Carbohydr. Res., 93 (1981) C6-C9) as promoters. The reaction is carried out in a suitable solvent such as chloroform, dichorometane, or toluene. When the monosaccharide derivative in question is a per-O-acylated glycosyl bromide or chloride, promotors such as silver trifluoromethane sulphonate or mercury (II)salts (H. Paulsen, Angew. Chem. Int. Ed. Engl., 21 (1982) 155-173) can be used and the reactions are carried out in a suitable solvent such, as dichlorometane or toluene. The glucose W1R1 or W1R1PG1-glycosides are obtained after de-O-acylation using sodium methoxide (A. Thompson, M. L. Wolfrom, and E. Pascu, page 215-220, Methods in Carbohydrate Chemistry, Vol II, Editors: R. L. Whistler and M. L., E. Wolfrom, Academic Press, New York, 1963) in methanol or in methanol containing a co-solvent such as dichlormethane or tetrahydrofurane.
The 4,6-(4xe2x80x2-methoxy)benzylidene acetals are then obtained by reaction with 4-methoxybenzaldehyde dimethyl acetal and acid in a polar non-protic solvent such as e.g. dimethyl formamide, acetonitrile or tetrahydrofurane (J. J. Patroni et al., Aust. J. Chem. 1988,(41),91-102; for other methods of acetal formation, see for example A. N. de Belder, 1979, adv. Carbohydr. Chem. Biochem., 34, 179 and references cited therein).
The epoxides B1 or B2 
are then obtained through sulphonate esters: The manno epoxides B1 can be prepared by reacting the glucoside derivative A with sodium hydride and p-toluenesulehonylimidazol in dimethylformamide (D. Hicks and E. Fraser-Reid; Synthesis 1974, 203) or with sodium hydride and p-toluenesulahonyl chloride in tetrahydrofurane (V. S. Murthy et al, Synthetic Commun. 1993, 23(3), 285-289).
The allo epoxides B2 can be prepared by reacting the glucoside derivative A with methylsulphonyl or p-toluenesulphonyl chloride in pyridine and treating the resulting methylsulphonate diester with sodium ethoxide in ethanol (Y. Ali, A. C. Richardson, Carbohydrate Res. 1967, 5, 441-448; N. Richtmeyer, Methods in Carbohydrate Chemistry, Vol 1,107).
The epoxides B1 or B2 can be reacted with suitable nucleophilic reagents to yield the diaxially substituted allo hexopyranosides C1 and C2 
(for general references on the use of epoxides, see e.g. J. Gorzynski Smith, Synthesis, 1984, 6, 629-656 Masamune S., Choy W., Petersen J S, and Sita L R, Angew. Chem. Int. Ed. Engl., 1985, 24, 1-76; A. S. Rao et al., Tetrahedron Lett., 1983, 39, 2323).
When the first atom of R2 and Z1 (as defined above) connected to the carbohydrate moiety in the desired final product is a nitrogen (=the nucleophilic atom), then the preferred nucleophile Nu1 or Nu2 is azide (N3xe2x88x92). The epoxide is treated with sodium azide and ammonium chloride in boiling 2-methoxy-ethanol (R. D. Guthrie and D. Murphy; J.Chem.Soc. 1963, 5288-5294).
When the nucleophilic atom is oxygen or sulphur, the preferred general method of epoxide opening involves treatment with suitably protected alcohol or thiol in the presence of neutral alumina in ether (G. H. Posner and D. Z. Rogers, J. Am. Chem. Soc. 1977, 99, 8208; G. H. Posner, D. Z. Rogers and A. Romero, Isr. J. Chem. 1979, 18, 259; and G. H. Posner, M. Hulce and R. K. Rose, Synth. Commun. 1981, 11, 737).
When the nucleophilic atom is carbon, the most commonly used reagents are organomagnesium, organolithium, organocopper, organoaluminium and organoboron compounds (J. Gorzynski Smith, Synthesis, 1984, 8, 629-656 and references cited therein).
When the product is an allo hexopyranoside C1, the 2-hydroxy function can either be blocked with a protective group that allows for the introduction of the R2 functionality at a later stage (preferred if R2 is an ester, not shown in figure), or the suitably protected, when necessary, functionality R2 is introduced to produce D1 
For example, OH-groups to ethers or esters (Protective Groups in Organic Synthesis, Editors T. W. Greene and P. G. M. Wuts, John Wiley and Sons, Inc., New York, 1991); OH-groups to carbonates (J. March, Advanced Organic Chemistry-Reaction Mechanisms, and Structure, 3rd Edn. John Wiley and Sons, New York, 347 (1985), and references cited therein); OH-groups to carbamates (J. March, Advanced Organic Chemistry-Reaction Mechanisms, and Structure, 3rd Edn. John Wiley and Sons, New York, 791-792 (1985), and references cited therein); OH-groups to alkylgroups via exomethylene derivatives and subsequent hydrogenation or via other routes (H. O. H. House, Modern Synthetic Reactions, 2nd Edn. W. A Benjamin, Inc., Menlo Park, Calif. 1-130 (1972), and references cited therein; J. Yoshimura, Adv. Carbohydr. Chem Biochem., 42 (1984) 69-134); and exchange of OH-groups for heterocyclic groups, via different routes (A. R. Katritzky, Handbook of Heterocyclic Chemistry, Pergamon Press, Oxford, 1985).
When the product is an allo hexopyranoside C2, the 3-hydroxy function is blocked with a protective group that allows for the introduction of the Z1-R3 functionality at a later stage resulting in intermediates of the type D2 
(Protective Groups in Organic Synthesis, Editors T. W. Greene and P. G. M. Wuts, John Wiley and Sons, Inc., New York, 1991) or transformed to a manno hexopyranoside intermediate D3 
where Nu1 is a protected or masked form of the functionality Z1. OH-groups to ethers or esters (Protective Groups in Organic Synthesis, Editors T. W. Greene and P. G. M. Wuts, John Wiley and Sons, Inc., New York, 1991); OH-groups to azido-groups: J. March, Advanced Organic Chemistry-Reaction Mechanisms, and Structure, 3rd Edn. John Wiley and Sons, New York, 380, (1985), and references cited therein; H. H. Baer, Pure Appl. Chem., 61(7) (1989) 1217-1234, and references cited therein; OH-groups to aminogroups via azides or other routes (March, Advanced Organic Chemistry-Reaction Mechanisms, and Structure, 3rd Edn. John Wiley and Sons, New York, 1106, 798-800 (1985), and references cited therein; H. H. Baer, Pure Appl. Chem., 61(7) (1989) 1217-1234, and references cited therein).
The 4,6-O-acetal function is then reductively opened to yield either the function R6 in the case when R6 is an ether, or the intermediates F1, F2 or F3 with a hydroxy function on position 6 (reductive opening of acetals, see Garegg P J and Hultberg H, Carbohydr. Res. 1981, 93, c10-11; Garegg P J, Hultberg H, and Wallin S, Carbohydr. Res. 1982, 108, 97-101; Liptak A, Jodal I, Nanasi P, Carbobydr. Res. 1975, 44, 1-11; Baker D C, Horton D, Tindall C G, Methods in Carbohydr. Chem., 1976 Vol 6, 3-6; Mikami T, Asano H, Mitsunobu O, Chem. Lett. 1987, 10, 2033-2036; Ek M, Garegg P J, Hultberg H, Oscarsson S, J. Carbohydr. Chem. 1983, 2, 305-311; Hunter R, Bartels B, Michael J P, Tetrahedron Lett. 1991, 32, 1095-1098; Rao S P, Grindley T B, Carbohydr. Res. 1991, 218, 83-93; Hunter,R. Bartels,B. J. Chem. Soc. Chem. Commun. 1991, 2887-2888).
For example, the intermediates of type D1, D2 or D3 are treated with sodium cyanoborohydride and chlorotrimethylsilane in acetonitrile, (R. Johansson and B. Samuelsson, J. Chem. Soc. Perkin Trans. 1, 1984, 2371-2374) or borane-trimethylamine complex and aluminium trichloride. The regiochemical outcome of the reaction is often solvent-dependent (Ek M, Garegg P J, Hultberg H, Oscarsson S, J. Carbohydr. Chem. 1983, 2, 305-311).
The aldehyde intermediates of type G1, G2 or G3 
are obtained by oxidation of the corresponding 6-alcohol intermediates of type D1, D2 or D3, preferrably by the Swern procedure. (Mancuso A J, Swern D, Synthesis, 1981, 165-185; Tidwell T, Synthesis, 1990, 857-870; for other oxidation methods, see A. H. Haines, 1988, Methods for the Oxidation of Organic Compounds, Chapter 2, Academic Press, San Diego, and references cited therein).
In the next step a carbon nucleophile is added to the aldehyde function of the intermediates of type G1, G2 or G3. Preferrably, a suitably protected alkyllithium or aryllithium reagent or a gringard reagent is added to the aldehyde in an ether or hydrocarbon solvent to produce the secondary alcohols H1, H2 and H3: 
For reactions of aldehydes with organolithium and organomagnesium compounds, see J. March, Advanced Organic Chemistry-Reaction Mechanisms, and Structure, 3rd Edn. John Wiley and Sons, New York, 347 (1985), and references cited therein.
For reactions of aldehydes with organolithium and organomagnesium and other carbon nucleophils, see Evans D A, Aidrichim. Acta, 1982, 15, 23, and references cited therein.
For specific examples on the use and preparation of arylsubstituted phenyllithium and grignard reagents, see Ames M M, Castagnoli Jr. N, J. Labelled Compd., 1974, 10(2), 195-205; DE U.S. Pat. No. 3,807,910 A1; Mills R J, Snieckus V, Polynucl. Aromat. Hydrocarbons, [Pap. Int. Symp.], 8th, Meeting 1983, 913-24. Edited by: Cooke M and Dennis A J, Battelle Press 1985: Columbus, Ohio; Iriye R, Furukawa K, Nishida R, Kim C, Fukami H, Biosci. Biotechnol. Biochem. 1992, 56(11), 1773-5; Comber M F, Sargent M V U, J. Chem. Soc., Chem. Commun., 1991, (3), 190-2; Hirai T, Yoshizawa A, Nishiyama I, Fukumasa M, Shirxc3xa1tori . N, Yokoyama A, EP 341686 A2; Leeson P D, Emmett J C, Shah V P, Showell G A, Novelli R, Prain H D, Benson M G, Ellis D, Pearce N J, Underwood A H, J. Med. Chem.1989, 32(2), 320-36); Meltzer P C, Liang A Y, Brownell A L, Elmaleh D R, Madras B K, J. Med. Chem., 36(7), 855-62; Willard A K, Novello F C, Hoffman W F, Cragoe Jr E J. U.S. Pat. No. 4,459,423.
For substituted phenyllithium reagents that can be further elaborated into heterocyclic compounds, see: Lang H J,; Muschaweck R, AU 514406 B2; Lang H J, Muschaweck R, Hropot M, HU 19761; Lang H J, Muschaweck R, Hropot M, DE U.S. Pat. No. 2,737,195.
For heteroaromatic aryllithiums and grignard reagents, see: Yang Y, Martin A R, Nelson D L, Regan J, Heterocycles, 1992, 34(6), 1169-75.
For examples of other organometallic reagents for the stereo-selective synthesis of secondary alcohols from aldehydes:
Homoallyl alcohols with crotylmolybdenum complexes: Faller J W. John J A, Mazzieri M R, Tetrahedron Lett. 1989, 30, 1769-1772.
Homoallyl alcohols with titanium complexes: Riediker M, Duthaler R O, Angew. Chem. Int. Ed. Engl., 1989, 28, 494-495.
3-Pyrollyl alcohols with silyl protected 3-lithiopyrrole: Bray B L, Mathies P H, Naef R, Solas D R, Tidwell T T, Artis D R, Muchowski J M, J. Org. Chem., 1990, 55, 6317-6328.
Allylic alcohols with E-vinylalane: A P Kozikowski and Jiang-Ping Wu, Tetrahedron Lett. 1990, 30, 4309-4312 and references cited therein.
Trans-allylic diols with vinylstannanes: Corey E J, Wollenberg R H, J. Org. Chem., 1975, 40, 2265-2266.
Pyrrolidine carbinols with xcex1-lithio pyrrolidine amidines: Sanner M A, Tetrahedron Lett. 1989, 30, 1909-1912.
Organozinc reagents: Fxc3xcrstner A, Synthesis, 1989, 571-590, and references cited therein.
Thereafter, the substituent on the 3-position (Nu1 or OPG1) is transformed into a nucleophile in order to install the negatively charged functionality Z1-D-R3.
The secondary 6-alcohols H1, H2 and H3 are first protected, (Protective Groups in Organic Synthesis, Editors T. W. Greene and P. G. M. Wuts, John Wiley and Sons, Inc., New York, 1991) or transformed to amino functions in the cases where X1-R6 forms a peptide functionality (OH-groups to aminogroups via azides or other routes: See for examples March, Advanced Organic Chemistry-Reaction Mechanisms, and Structure, 3rd Edn. John Wiley and Sons, New York, 1106, 798-800 (1985), and references cited therein; H. H. Baer, Pure Appl. Chem., 61(7) (1989) 1217-1234, and references cited therein).
For peptide synthesis, see Gross and Meienhofer, The Peptides, 3 vol., Academic Press, New York,1979-1981; Grant G A et al., Synthetic Peptides, A Users Guide, 1992, W. A. Freeman and Company, New York, and references cited therein).
The 3-position is deprotected to an alcohol, thiol or amine intermediate I1, I2 or I3 
(Protective Groups in Organic Synthesis, Editors T. W. Greene and P. G. M. Wuts, John Wiley and Sons, Inc., New York, 1991, and references cited therein).
For example, treatment of I1, where R2-PG1 is a combination of ether functions and Q1 is azide, with gaseous hydrogen sulphide in pyridine and water (T. Adashi, Y. Yamada, I. Inoue and M. Saneyoshi, Synthesis, 1977, 45). For other methods of azide reductions, see Poopeiko N E, Pricota T I, Mikhailopulo I A, Synlett, 1991, 5, 342; Samano M C, Robins M J, Tetrahedron Lett. 1991, 32, 6293-6296; Rakotomanomana N, Lacombe J-M, Pavia A, Carbohydr. Res., 1990, 197, 318-323; Malik A A, Preston S B, Archibald T G, Cohen M P, Baum K, Synthesis, 1989,450-451; Maiti S, Spevak P, Reddy N, Synt. Commun. 1988, 18, 1201-1206; Bayley H, Standring D N, Knowles J R, Tetrahedron Lett., 1978, 39, 3633-3634).
The intermediates I1, I2 or I3 are sulphated with sulphur trioxide-pyridine or -triethylamine complex to obtain the intermediates J2, J4 and J6 
(see, for example J. Basten, G. Jaurand, B. Olde-Hanter, M. Petitou and C.A.A. van Boeckel, Bioorg. Med. Chem. Lett, 1992, 2(9), 901-904 and references cited therein; J.Basten, G. Jaurand, B. Olde-Hanter, P. Duchaussoy, M. Petitou and C. A. A. van Boeckel, Bioorg. Med. Chem. Lett, 1992, 2(9), 905-910, and references cited therein; Bxc3x6cker, T. Lindhorst, T K. Thiem, J. Vill, V. Carbohydr. Res. 1992, 230, 245-256) or coupled to form the phosphoester intermediates J1, J3 and J5 
Since the phosphorus-nitrogen bond is known to be acid labile, the intermediates leading to phosphodiester end-products are preferred (M. Selim and T. N. Thanh, C.R. Seances Acad. Sci, 1960, 250, 2377).
For example, the alcohol intermediates I1, I2 or I3 are treated with 2,2,2-trichloroethyl 2-chlorophenyl phosphochloridate in chloroform and pyridine to form the phosphate triesters. The 2,2,2-trichloroethyl group is removed by treatment with zinc powder and the resulting phosphate diester is activated with 3-nitro-1-(2,4,6-triisopropylbenzenesulphonyl)-1,2,4-triazol e and coupled with the alcohol R3-OH to form the intermediates J1, J3 and J5. The 2-chlorophenyl group is removed by treatment with pyridine-2-aldoxime and N,N,N,N-tetramethylguanidine in moist pyridine (see for example P. J. Garegg, R. Johansson, I. Lindh and B. Samuelsson, Carbohydr. Res. 1986, 150, 285-289).
Alternatively, by the phosphite triester approach, alcohol intermediates I1, I2 or I3 are treated with phenyl chloro-N,N-diisopropylphosphoramidite in acetonitrile to form carbohydrate phosphoamidites. After purification by chromatography, these are exposed to an alcohol R3xe2x80x94OH in the presence of a mild acid, such as pyridinium p-toluenesulphonate and treated with tert-butyl hydroperoxide to form phosphate diesters J1, J3 and J5 (PG3 =H) (H-N. Caro, M. Martxc3xadn-Lomas and M. Bernabxc3xa9, Carbohydr. Res. 1993, 240, 119-131, and references cited therein).
For a review on phospodiesters in DNA synthesis, see Narang S, Tetrahedron, 1983, 39, 1-22 and D. W. Hutchinson, 1991, Chapter 3 in Chemistry of Nucleosides and Nucleotides, vol 2, ed. B. Townsend, Plenum Press, New York, and references cited therein. For other examples on carbohydrate phosphodiester synthesis, see for example Ichikawa Y, Sim M M, Wong C H, J. Org. Chem. 1992, 57, 2943-2946 and Schmidt R R, Braun H, Jung K-H, Tetrahedron Lett. 1992, 33, 1585-1588. For synthesis of modified phosphodiester linkages, See R. S. Varma, 1993, Synlett, 621-636, and references cited therein.
To obtain arylphosphonic acid esters and amides J1, J3 and J5, where R3 is an alkyl or aromatic group the arylphosphonic acid R3-PO3H2 is coupled to the alcohol intermediates I1, I2 or I3, for example, with a carbodiimide reagent, or treatment of the phosphonic dichlorides with the alcohol intermediates I1, I2 or I3 in pyridine (T. H. Siddal III, and C. A. Prohaska, J. Am. Chem. 1962, 84, 3467).
The alkylphosphonic triesters are formed from trialkyphosphites and alkyl halides by the Arbuzov reaction (Arbuzov, Pure Appl. Chem. 1964, 9, 307-335, J. March, Advanced Organic Chemistry-Reaction Mechanisms, and Structure, 3rd Edn. John Wiley and Sons, New York, 347 (1985), and references cited therein).
For the preparation of arylphosphonic triesters via phosphorus trichloride, see for example: K. Sasse, Methoden der Organichen Chemie (Houben-Weyl), 4th ed., Vol. 12/1, Georg Thieme, Stuttgart, 1963, p. 314 and p. 392 and references cited therein; G. M. Kosolapoff, Org. React. 6, 273 (1951), and references cited therein; L. D. Freedman and G. O. Doak, Chem. Rev. 1957, 57, 479, and references cited therein.
For the preparation of arylphosphonic triesters via organomagnesium or organolithium reagents, see for example: K. Sasse, Methoden der Organichen Chemie (Houben-Weyl), 4th ed., Vol. 12/1, Georg Thieme, Stuttgart, 1963, p. 372, and references cited therein; G. M. Kosolapoff, Org. React. 6, 273 (1951), and references cited therein.
Intermediates J1, J2, J3, J4, J5 and J6 are deprotected to form the final products (Protective Groups in organic Synthesis, Editors T. W. Greene and P. G. M. Wuts, John Wiley and Sons, Inc., New York, 1991, and references cited therein) and transformed to their sodium or potassium salts.
It is justified to assume that the compounds described above are capable of interacting with sites in PapD and other periplasmic chaperones. In order to establish that this is really the case, assays like those described in the examples should be performed.
Thus, a preferred compound of the invention is a compound as described above, which causes a prevention, inhibition or enhancement of the binding of G1xe2x80x2-19xe2x80x2WT to PapD, and/or causes a prevention, inhibition or enhancement of the binding of the fusion peptide MBP-G1xe2x80x2-140xe2x80x2 to PapD and/or causes a prevention, inhibition or enhancement of the binding of the peptide G125xe2x80x2-140xe2x80x2 (which have the sequence SEQ ID NO: 20) to PapD and/or is capable of inhibiting the restoration of the PapD-PapG complex normally caused by the addition of access PapD.
The assay used to establish that a substance exhibits one of the above effects is preferably one of the assays described in the examples herein. Of course, also. other assays as those discussed above in the methods of the invention may be utilized in order to establish that the compound actually is capable of inhibiting pilus assembly.
One important point which should be taken into consideration when setting up an assay, is the role the chaperones are playing in vivo. They bind to the pilus subunits already during the transport through the cell membrane of the subunits and it is therefore assumed, that the pilus subunits are more or less unfolded (i.e. not in their final folded conformation) when they bind to the chaperone. It has been observed by the inventors that the kinetics of binding between completely folded pilus subunits (or analogues thereof) and the chaperone PapD is a slow process, although it is known that the process of pilus assembly is relatively fast in vivo. In order to speed up the rate of assembly of the chaperone/pilus subunit complex in vitro it is contemplated that more or less severe denaturing conditions could be imposed on the pilus subunits (or the analogues thereof) prior to the assay. Such denaturing could be obtained by subjecting the pilus subunits to physical stress (e.g. to elevated temperature, pressure changes, radiation etc.) or to changes in the chemical environment (e.g. changes in ionic strength, changes in pH, or the addition of denaturing compounds or disulphide reducing compounds.
The expression xe2x80x9cdenaturing compoundxe2x80x9d refers to a compound which when present as one of the solutes in a liquid phase comprising polypeptide molecules may destabilize folded states of the polypeptide molecules leading to partial or complete unfolding of the polypeptide chains. The denaturing effect exerted by a denaturing compound increases with increasing concentration of the denaturing compound in the solution, but may furthermore be enhanced or moderated due to the presence of other solutes in the solution, or by changes in physical parameters, e.g. temperature or pressure.
As examples of suitable denaturing compounds to be used may be mentioned urea, guanidine-HCl, di-C1-6alkylformamides such as dimethylformamide and di-C1-6-alkylsulphones.
Examples of disulphide reducing compounds are glutathionyl-2-thiopyridyl disulphide, 2-thiocholyl-2-thiopyridyl disulphide, 2-mercaptoethanol-2-thiopyridyl disulphide and mercaptoacetate-2-thiopyridyl disulphide.
A set of observations confirm the assumption that the pilus subunits are more or less unfolded while bound to the chaperone: As described in Kuehn et al., 1991, it is possible to restore the PapD-PapG complex after denaturation by adding access PapD. Further, preliminary results obtained by capillary electrophoresis show that denaturation of the fusion protein MBP-G1xe2x80x2-140xe2x80x2 gives a single form of the fusion protein, whereas two forms of the fusion protein are observed in capillary electrophoresis before denaturation, one major which is unable to interact with PapD and one minor which is capable of interacting with PapD. It is therefore contemplated that the denatured fusion protein may serve as a superior substrate in the different competitive assays described herein as does the non-denatured form of the fusion protein.
Thus, in a preferred embodiment of the invention, the compound of the invention causes a prevention, inhibition or enhancement of the binding of a denatured form of either a pilus subunit or an analogue thereof to PapD, and/or causes a prevention, inhibition or enhancement of the binding of a denatured form of MBP-G1xe2x80x2-140xe2x80x2 to PapD and/or causes a prevention, inhibition or enhancement of the binding of a denatured form of G125xe2x80x2-140xe2x80x2 to PapD.
As will appear from the examples, compounds which should be capable of interacting with PapD and other chaperones have already been identified and synthesized. These compounds which are all pyranosides are also an important part of the invention:
Ethyl 2,3-O-Dibenzoyl-4-O-benzyl-1-thio-xcex2-D-glucohexopyranoside;
Ethyl 6-O-acetyl-2,3-O-dibenzoyl-4-O-benzyl-1-thio-xcex2-D-glucohexopyranoside;
Methylglycolyl 6-O-acetyl-2,3-O-dibenzoyl-4-O-benzyl-xcex2-D-glucohexopyranoside;
2-(Hydroxy)ethyl 4-O-benzyl-xcex2-D-glucopyranoside;
Sodium glycolyl 4-O-benzyl-xcex2-D-glucohexopyranoside;
Methyl 2-O-ethyl-4,6-O-(4xe2x80x2-methoxy)phenylmethylene-xcex1-D-mannohexopyranoside;
Methyl 2-O-ethyl-3-O-dimethyl-t-butylsilyl-4,6-O-(4xe2x80x2-methoxy)phenylmethylene-xcex1-D-mannohexopyranoside;
Methyl 2-O-ethyl-3-O-dimethyl-t-butylsilyl-4,-O-(4xe2x80x2-methoxy)benzyl-xcex1-D-mannohexopyranoside;
methyl 2-O-ethyl-3-O-dimethyl-t-butylsilyl-6-O-(4xe2x80x2-methoxy)benzyl-xcex1-D-mannohexopyranoside;
Methyl 2-O-ethyl-3-O-dimethyl-t-butylsilyl-4,-O-(4xe2x80x2-methoxy)benzyl-6(S)-phenyl-xcex1-D-mannohexopyranoside;
Methyl 2,3-anhydro-4,6-O-p-methoxybenzylidene-xcex1-D-mannopyranoside;
Methyl 3-azido-4,6-O-p-methoxybenzylidene-xcex1-D-altropyranoside;
Methyl 3-azido-2-O-ethyl-4,6-O-p-methoxybenzylidene-xcex1-D-altropyranoside;
Methyl 3-azido-3-deoxy-2-O-ethyl-4-O-p-methoxybenzyl-xcex1-D-altropyranosid;
Methyl 3-azido-6-O-benzoyl-3-deoxy-2-O-ethyl-4-O-p-methoxy-benzyl-xcex1-D-altropyranoside;
Methyl 6-O-benzoyl-3-deoxy-2-O-ethyl-4-O-p-methoxybenzyl-3-sulfamino-xcex1-D-altropyranoside sodium salt;
Methyl 6-O-benzoyl-3-deoxy-2-O-ethyl-3-sulfamino-xcex1-D-altropyranoside ammonium salt;
Methyl 3-azido-6-O-pivaloyl-3-deoxy-2-O-ethyl-4-O-p-methoxy-benzyl-xcex1-D-altropyranoside;
Methyl 6-O-pivaloyl-3-deoxy-2-O-ethyl-4-O-p-methoxybenzyl-3-sulfamino-xcex1-D-altropyranoside sodium salt;
Methyl 6-O-pivaloyl-3-deoxy-2-O-ethyl-3-sulfamino-xcex1-D-altropyranoside ammonium salt;
Methyl 6-O-pivaloyl-3-deoxy-2-O-ethyl-4-O-p-methoxybenzyl-3-tbutyloxamido-xcex1-D-altropyranoside;
Methyl 6-O-pivaloyl-3-deoxy-2-O-ethyl-3-oxamido-xcex1-D-altropyranoside ammonium salt;
Methyl 3-azido-6-O-pyrrol-3xe2x80x2-ylcarboxyl-3-deoxy-2-O-ethyl-4-O-p-methoxybenzyl-xcex1-D-altropyranoside; and
Methyl 6-O-pyrrol-3xe2x80x2-ylcarboxyl-3-deoxy-2-O-ethyl-3-sulfamino-xcex1-D-altropyranoside ammonium salt.
Other compounds are of course also possible as interactors with sites in chaperones. As is evident from example 7, modified peptides also may prove to be useful in the methods of the invention.
As will be clear from the above, the identification of a site in the chaperone which may be affected so as to interfere with pilus assembly is a critical starting point in the methods described herein for the identification, isolation and synthesis of compounds capable of interacting with periplasmic chaperones.
Thus, the invention also relates to a method for identifying a binding site in a molecular chaperone, comprising
co-crystallizing the periplasmic molecular chaperone or an analogue thereof with a ligand binding to the periplasmic molecular chaperone or the analogue thereof,
resolving the three-dimensional structure of the chaperone/ligand interaction, thereby resolving the three-dimensional structure of the periplasmic molecular chaperone or the analogue thereof when binding to the ligand,
determining the site-point(s) involved in the intermolecular interaction between the periplasmic molecular chaperone or the analogue thereof and the ligand, and
identifying the thus determined site-point(s) of the periplasmic molecular chaperone or the analogue thereof as a binding site in the periplasmic molecular chaperone or the analogue thereof.
By the term xe2x80x9cligandxe2x80x9d as used herein, is meant a substance which exhibit binding to a host or receptor molecule (in this connection a chaperone). The binding is not a non-specific interaction, which means that a binding motif between the ligand and the host or receptor molecule exists. In other words, when bringing a sample of the ligand and a sample of the host or receptor molecule in contact with each other the complexes formed between the ligand and the host or receptor molecule will substantially all reflect the same intermolecular interactions.
As mentioned above one embodiment of the invention is to administer a substance which is capable of preventing, inhibiting or enhancing binding between pilus subunits and molecular chaperones.
Accordingly the invention relates to a pharmaceutical composition, comprising, as an active compound, a substance capable of interacting with at least one type of periplasmic molecular chaperone which binds pilus subunits during transport of these pilus subunits through the periplasmic space and/or during the process of assembly of the intact pilus, in such a manner that binding of pilus subunits to the periplasmic molecular chaperone is prevented, inhibited or enhanced, in combination with at least one pharmaceutically acceptable carrier or excipient. Preferably such a substance is a substance according to the invention or a substance identified/designed according to the methods of the invention.
The pharmaceuticals and pharmaceuticals discussed herein are thus, according to the invention, for the treatment and/or prophylaxis of the same conditions as those discussed when disclosing the method of treatment of the invention and caused by the same bacterial species.
Therefore, a pharmaceutical composition, comprising, as an active compound, a substance used in the therapeutic methods of the invention, a substance according to the invention or a substance identified according to the methods of the invention, in combination with at least one pharmaceutically acceptable carrier or excipient, is a part of the invention.
Such pharmaceutical compositions of the invention could also comprise at least one additional pharmaceutical substance, which i.a. could enhance the pharmaceutical effects exerted by the substance of the invention or the substance identified according to the invention.
Additional pharmaceutical substances could be steroid hormones, disinfectants, anti-pyrretics, etc. Preferably such an additional substance could be an antibacterial agent.
Such an anti-bacterial agent could conveniently be selected from the group consisting of penicillins, cephalosporins, aminoglycosides, sulfonamides, tetracyclines, chloramphenicol, polymyxins, antimycobacterial drugs and urinary antiseptics.
The invention also relates to a substance employed in the methods of the invention as well as a substance of the invention and a substance identified according to the methods of the invention for use as a pharmaceutical. It is preferred that the pharmaceutical is for anti-bacterial treatment and/or prophylaxis, especially treatment and/or prophylaxis of diseases caused by tissue-adhering pilus forming bacteria, and it is especially preferred that the pharmaceutical is for treatment and/or prophyloxis of urinary tract infection.
Finally, the invention relates to the use of a substance employed in the methods of the invention as well as a substance of the invention and of a substance identified according to the methods of the invention for the preparation of a pharmaceutical composition for the treatment and/or prophylaxis of bacterial infection.